Methods utilizing scanning probe microscope tips and products therefor or produced thereby

ABSTRACT

The invention provides a lithographic method referred to as “dip pen” nanolithography (DPN). DPN utilizes a scanning probe microscope (SPM) tip (e.g., an atomic force microscope (AFM) tip) as a “pen,” a solid-state substrate (e.g., gold) as “paper,” and molecules with a chemical affinity for the solid-state substratte as “ink.” Capillary transport of molecules from the SPM tip to thee solid substrate is used in DPN to directly write patterns consisting of a relatively small collection of molecules in submicrometer dimensions, making DPN useful in the facrication of a variety of microscale and nanoscale devices. The invention also provices substrates patterened by DPN, including submirocmeter combinatorial arrays, and kits, devices and software for performing DPN. The invention further provides a method of performing AFM imaging in air. The method comprises coating an AFM tip with a hydrophobic compound, the hydrophobic compoind being selected so that AFM imaging perfromed using the coated AFM tipn is improved compared to AFM imaging preformed using an uncoated AFM tip. Finally, the invention provides AFM tips coated with the hydrophobic compounds.

This application is a continuation application of Ser. No. 10/212,217filed Aug. 6, 2002, the complete disclosure of which is incorporated byreference in its entirety; which is a continuation application of Ser.No. 09/866,533 filed May 24, 2001, the complete disclosure of which isincorporated by reference in its entirety; which claims priority toprovisional applications 60/207,711 and 60/207,713 filed May 26, 2000,the complete disclosures of which are incorporated by reference in theirentirety; Ser. No. 09/866,533 also is a continuation-in-part of Ser. No.09/477,997 filed Jan. 5, 2000, the complete disclosure of which isincorporated by reference in its entirety; which claims priority toprovisional applications 60/115,133 filed Jan. 7, 1999 and 60/1 57,633filed Oct. 4, 1999, the complete disclosures of which are incorporatedby reference in their entirety.

This invention was made with government support under grantF49620-96-1-055 from the Air Force Office Of Science Research. Thegovernment has rights in the invention.

FIELD OF THE INVENTION

This invention relates to methods of microfabrication andnanofabrication. The invention also relates to methods of performingatomic force microscope imaging.

BACKGROUND OF THE INVENTION

Lithographic methods are at the heart of modern day microfabrication,nanotechnology and molecular electronics. These methods often rely onpatterning a resistive film, followed by a chemical etch of thesubstrate.

Dip pen technology, where ink on a sharp object is transported to apaper substrate by capillary forces, is approximately 4000 years old.Ewing, The Fountain Pen: A Collector's Companion (Running Press BookPublishers, Philadelphia, 1997). It has been used extensively throughouthistory to transport molecules on macroscale dimensions.

By the present invention, these two related but, with regard to scaleand transport mechanism, disparate concepts have been merged to create“dip pen” nanolithography (DPN). DPN utilizes a scanning probemicroscope (SPM) tip (e.g., an atomic force microscope (AFM) tip) as a“nib” or “pen,” a solid-state substrate (e.g., gold) as “paper,” andmolecules with a chemical affinity for the solid-state substrate as“ink.” Capillary transport of molecules from the tip to the solidsubstrate is used in DPN to directly write patterns consisting of arelatively small collection of molecules in submicrometer dimensions.

DPN is not the only lithographic method that allows one to directlytransport molecules to substrates of interest in a positive printingmode. For example, microcontact printing, which uses an elastomer stamp,can deposit patterns of thiol-functionalized molecules directly ontogold substrates. Xia et al., Angew. Chem. Int. Ed. Engl., 37:550 (1998);Kim et al., Nature, 376:581 (1995); Xia et al., Science, 273:347 (1996);Yan et al., J. Am. Chem. Soc., 120:6179 (1998); Kumar et al., J. Am.Chem. Soc., 114:9188 (1992). This method is a parallel technique to DPN,allowing one to deposit an entire pattern or series of patterns on asubstrate of interest in one step. In contrast, DPN allows one toselectively place different types of molecules at specific sites withina particular type of nanostructure. In this regard, DPN complementsmicrocontact printing and many other existing methods of micro- andnanofabrication.

There are also a variety of negative printing techniques that rely onscanning probe instruments, electron beams, or molecular beams topattern substrates using self-assembling monolayers and other organicmaterials as resist layers (i.e., to remove material for subsequentprocessing or adsorption steps). Bottomley, Anal. Chem., 70:425R (1998);Nyffenegger et al., Chem. Rev., 97:1195 (1997); Berggren et al.,Science, 269:1255 (1995); Sondag-Huethorst et al., Appl. Phys. Lett.,64:285 (1994); Schoer et al., Langmuir, 13:2323 (1997); Xu et al.,Langmuir, 13:127 (1997); Perkins et al., Appl. Phys. Lett., 68:550(1996); Carr et al., J. Vac. Sci. Technol. A, 15:1446 (1997); Lercel etal., Appl. Phys. Lett., 68:1504 (1996); Sugimura et al., J. Vac. Sci.Technol. A, 14:1223 (1996); Komeda et al., J. Vac. Sci. Technol. A,16:1680 (1998); Muller et al., J. Vac. Sci. Technol. B, 13:2846 (1995);Kimet et al., Science, 257:375 (1992). However, DPN can deliverrelatively small amounts of a molecular substance to a substrate in ananolithographic fashion that does not rely on a resist, a stamp,complicated processing methods, or sophisticated noncommercialinstrumentation.

A problem that has plagued AFM since its invention is the narrow gapcapillary formed between an AFM tip and sample when an experiment isconducted in air which condenses water from the ambient andsignificantly influences imaging experiments, especially thoseattempting to achieve nanometer or even angstrom resolution. Xu et al.,J. Phys. Chem. B, 102:540 (1998); Binggeli et al., Appl. Phys. Lett,65:415 (1994); Fujihira et al., Chem. Lett., 499 (1996); Piner et al.,Langmuir, 13:6864 (1997). It has been shown that this is a dynamicproblem, and water, depending upon relative humidity and substratewetting properties, will either be transported from the substrate to thetip or vice versa. In the latter case, metastable,nanometer-length-scale patterns, could be formed from very thin layersof water deposited from the AFM tip (Piner et al., Langmuir, 13:6864(1997)). The present invention shows that, when the transportedmolecules can anchor themselves to the substrate, stable surfacestructures are formed, resulting in a new type of nanolithography, DPN.

The present invention also overcomes the problems caused by the watercondensation that occurs when performing AFM. In particular, it has beenfound that the resolution of AFM is improved considerably when the AFMtip is coated with certain hydrophobic compounds prior to performingAFM.

SUMMARY OF THE INVENTION

As noted above, the invention provides a method of lithography referredto as “dip pen” nanolithography, or DPN. DPN is a direct-write,nanolithography technique by which molecules are delivered to asubstrate of interest in a positive printing mode. DPN utilizes a solidsubstrate as the “paper” and a scanning probe microscope (SPM) tip(e.g., an atomic force microscope (AFM) tip) as the “pen”. The tip iscoated with a patterning compound (the “ink”), and the coated tip iscontacted with the substrate so that the patterning compound is appliedto the substrate to produce a desired pattern. The molecules of thepatterning compound are delivered from the tip to the substrate bycapillary transport. DPN is useful in the fabrication of a variety ofmicroscale and nanoscale devices. The invention also provides substratespatterned by DPN, including combinatorial arrays, and kits, devices andsoftware for performing DPN.

The invention further provides a method of performing AFM imaging inair. The method comprises coating an AFM tip with a hydrophobiccompound. Then, AFM imaging is performed in air using the coated tip.The hydrophobic compound is selected so that AFM imaging performed usingthe coated AFM tip is improved compared to AFM imaging performed usingan uncoated AFM tip. Finally, the invention provides AFM tips coatedwith the hydrophobic compounds.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Schematic representation of “dip pen” nanolithography (DPN). Awater meniscus forms between the atomic force microscope (AFM) tipcoated with 1-octadecanethiol (ODT) and the gold (Au) substrate. Thesize of the meniscus, which is controlled by relative humidity, affectsthe ODT transport rate, the effective tip substrate contact area, andDPN resolution.

FIG. 2A. Lateral force image of a 1 μm by 1 μm square of ODT depositedonto a Au substrate by DPN. This pattern was generated by scanning the 1μm² area at a scan rate of 1 Hz for a period of 10 mm at a relativehumidity of 39%. Then the scan size was increased to 3 μm. and the scanrate was increased to 4 Hz while recording the image. The faster scanrate prevents ODT transport.

FIG. 2B. Lattice resolved, lateral force image of an ODT self-assemblingmonolayer (SAM) deposited onto a Au(111)/mica substrate by DPN. Theimage has been filtered with a fast fourier transform (FFT), and the FFTof the raw data is shown in the lower right insert. The monolayer wasgenerated by scanning a 1000 Å square area of the Au(111)/mica substratefive times at a rate of 9 Hz under 39% relative humidity.

FIG. 2C. Lateral force image of 30 nm wide line (3 μm long) depositedonto a Au/mica substrate by DPN. The line was generated by scanning thetip in a vertical line repeatedly for five minutes at a scan rate of 1Hz.

FIG. 2D. Lateral force image of a 100 nm line deposited on a Ausubstrate by DPN. The method of depositing this line is analogous tothat used to generate the image in FIG. 2C, but the writing time was 1.5minutes. Note that in all images (FIGS. 2A-2D), darker regionscorrespond to areas of relatively lower friction.

FIG. 3A. Lateral force image of a Au substrate after an AFM tip, whichhas been coated with ODT, has been in contact with the substrate for 2,4, and 16 min (left to right). The relative humidity was held constantat 45%, and the image was recorded at a scan rate of 4 Hz.

FIG. 3B. Lateral force image of 16-mercaptohexadecanoic acid (MHDA) dotson a Au substrate. To generate the dots, a MHDA-coated AFM tip was heldon the Au substrate for 10, 20, and 40 seconds (left to right). Therelative humidity was 35%. Note that the transport properties of MHDAand ODT differ substantially.

FIG. 3C. Lateral force image of an array of dots generated by DPN. Eachdot was generated by holding an ODT-coated tip in contact with thesurface for ˜20 seconds. Writing and recording conditions were the sameas in FIG. 3A.

FIG. 3D. Lateral force image of a molecule-based grid. Each line, 100 nmin width and 2 μm in length, required 1.5 minutes to write.

FIGS. 4A-B. Oscilloscope recordings of lateral force detector outputbefore the AFM tip was coated with 1-dodecylamine (FIG. 4A) and afterthe tip had been coated with 1-dodecylamine (FIG. 4B). The time of therecording spans four scan lines. Since the signal was recorded duringboth left and right scans, the heights of the square waves are directlyproportional to the friction. The Y-axis zero has been shifted forclarity.

FIGS. 5A-B. Lateral force images showing water transported to a glasssubstrate (dark area) by an unmodified AFM tip (FIG. 5A) and the resultof the same experiment performed with a 1-dodecylamine-coated tip (FIG.5B). Height bars are in arbitrary units.

FIG. 6A. Lattice resolved, lateral force image of a mica surface with a1-dodecylamine-coated tip. The 2D fourier transform is in the insert.

FIG. 6B. Lattice resolved, lateral force image of an self-assembledmonolayer of 11-mercapto-1-undecanol. This image has been fouriertransform filtered (FFT), and the FFT of the raw data is shown in lowerright insert. Scale bars are arbitrary.

FIG. 6C. Topographic image of water condensation on mica at 30% relativehumidity. The height bar is 5 Å.

FIG. 6D. Lateral force image of water condensation on mica at 30%relative humidity (same spot as in FIG. 6C).

FIGS. 7A-B. Topographic images of latex spheres, showing no changesbefore and after modifying tip with 1-dodecylamine. Height bars are 0.1μm. FIG. 7A was recorded with a clean tip, and FIG. 7B was recorded withthe same tip coated with 1-dodecylamine.

FIGS. 8A-B. Images of a Si₃N₄ surface coated with 1-dodecylaminemolecules, showing uniform coating. FIG. 8A shows the topography of aSi₃N₄ wafer surface that has been coated with the 1-dodecylaminemolecules, which has similar features as before coating. Height bar is700 Å. FIG. 8B shows the same area recorded in lateral force mode,showing no distinctive friction variation.

FIGS. 9A-C. Schematic diagrams with lateral force microscopy (LFM)images of nanoscale molecular dots showing the “essential factors” fornanometer scale multiple patterning by DPN. Scale bar is 100 nm. FIG. 9Ashows a first pattern of 15 nm diameter 1,16-mercaptohexadecanoic acid(MHA) dots on Au (111) imaged by LFM with the MHA-coated tip used tomake the dots. FIG. 9B shows a second pattern written by DPN using acoordinate for the second pattern calculated based on the LFM image ofthe first pattern shown in FIG. 9A. FIG. 9C shows the final patterncomprising both the first and- second patterns. The elapsed time betweenforming the two patterns was 10 minutes.

FIGS. 10A-C. For these figures, scale bar is 100 nm. FIG. 10A shows afirst pattern comprised of 50 nm width lines and alignment marksgenerated with MHA molecules by DPN. FIG. 10B shows a second patterngenerated with ODT molecules. The coordinates of the second pattern wereadjusted based on the LFM image of the MHA alignment pattern. The firstline patterns were not imaged to prevent the possible contamination bythe second molecules. FIG. 10C shows the final results comprisinginterdigitated 50 nm width lines separated by 70 nm.

FIG. 11A. Letters drawn by DPN with MHA molecules on amorphous goldsurface. Scale bar is 100 nm, and the line width is 15 nm.

FIG. 11B. Polygons drawn by DPN with MHA molecules on amorphous goldsurface. ODT molecules were overwritten around the polygons. Scale baris 1 μm, and the line width is 100 nm.

FIG. 12. A schematic representation of a DPN deposition and multi-stageetching procedure used to prepare three-dimensional architectures inAu/Ti/Si substrates. Panel (a): Deposition of ODT onto the Au surface ofthe multilayer substrate using DPN. Panel (b): Selective Au/Ti etchingwith ferri/ferrocyanide-based etchant. Panel (c): Selective Ti/SiO₂etching and Si passivation with HF. Panel (d): Selective Si etching withbasic etchant and passivation of Si surface with HF. Panel (e): Removalof residual Au and metal oxides with aqua regia and passivation of Sisurface with HF.

FIG. 13A-C. Nanometer scale pillars prepared according to FIG. 12,Panels a-d. FIG. 13A: AFM topography image after treatment of waferpatterned with 4 dots with 2 second deposition time. Pillar height is 55nm. The identification letter and top diameter (nm) are the following:A, 65; B, 110; C, 75; D, 105. Recorded at a scan rate of 2 Hz. FIG. 13B:The AFM topography image of a pillar on the same chip. Pillar height is55 nm. Recorded at a scan rate of 1 Hz. FIG. 13C: The cross-sectionaltrace of the AFM topography image through the pillar diameter.

FIGS. 14A-C. Nanometer scale lines prepared according to FIG. 12, Panelsa-d. FIG. 14A: AFM topography image after treatment of wafer patternedwith 3 lines of ODT at a rate of 0.4 μm/second. Line height is 55 nm.Recorded at a rate of 0.5 Hz. FIG. 14B: AFM topography image of a lineon the same chip. Line height is 55 mm. Recorded at a rate of 0.5 Hz.FIG. 14C: Cross-sectional topography trace of the line.

FIGS. 15A-C. Pillars prepared according to FIG. 12, Panels a-d. FIG.15A: An ODT-coated AFM tip was held in contact with the surface forvarious times to generate ODT dots of increasing size. Three-dimensionalfeatures with a height of 80 nm were yielded after etching. Theidentification letter, time of ODT deposition (seconds), estimateddiameter of ODT dot (nm), top diameter after etching (nm), and basediameter after etching (nm) are the following: A, 0.062, 90, 147, 514;B, 0.125, 140, 176, 535; C, 0.25, 195, 253, 491; D, 0.5, 275, 314, 780;E, 1, 390, 403, 892; F, 2, 555, 517, 982; G, 4, 780, 770, 1120; H, 8,1110, 1010, 1430; I, 16, 1565, 1470, 1910. FIG. 15B: SEM of samepillars. FIG. 15C: Top diameter plotted as a function of ODT depositiontime.

FIGS. 16A-B. Lines prepared according to FIG. 12, Panels a-d. FIG. 16A:The AFM topography image of lines on the same chip as used forpreparation of the pillars shown in FIG. 15. An ODT-coated AFM tip wasused to generate lines on the surface with various speeds to generatevarious sized ODT lines. The three-dimensional features shown in FIG.16A with a height of 80 nm were yielded after etching. Theidentification letter, speed of ODT deposition (μm/second), top linewidth after etching (nm), and base width are the following: A, 2.8, 45,45, 213; B, 50, 2.4, 70, 402; C, 60, 2.0, 75, 420; D, 1,6, 75, 90, 430;F, 1.2, 100, 120, 454; F, 150, 0.8, 150, 488; G, 0.4, 300, 255, 628, H,0.2, 600, 505, 942. FIG. 16B: SEM of the same lines.

FIG. 17: Diagram illustrating the components of a DPN nanoplotter andparallel writing.

FIG. 18: Diagram of an array of AFM tips for parallel writing.

FIG. 19: ODT nanodot and line features on Au generated by the same tipbut under different tip-substrate contact forces. There is less than 10%variation in feature size.

FIGS. 20A-B: Parallel DPN writing using two tips and a single feedbacksystem. FIG. 20A: Two nearly identical ODT patterns generated on Au inparallel fashion with a two pen cantilever. FIG. 20B: Two nearlyidentical patterns generated on Au in parallel fashion with a two pencantilever, each pen being coated with a different ink. The pattern onthe left is generated from an MHA-coated tip and exhibits a higherlateral force than the Au substrate. The pattern on the right wasgenerated with an ODT coated tip and exhibits a lower lateral force thanthe Au substrate.

FIGS. 21A-C: Nanoplotter-generated patterns which consist of featurescomprised of two different inks, ODT and MHA. The patterns weregenerated without removing the multiple-pen cantilever from theinstrument. FIG. 21A: Two-ink, cross-shaped pattern (ODT vertical linesand MHA horizontal lines) with an MHA dot in the center of the pattern(note the circular shape of the dot). FIG. 21B: A molecular cross-shapedcorral made of ODT. MHA molecules introduced into the center of thecorral diffuse from the center of the corral but are blocked when theyreach the 80 nm-wide ODT walls. Note the convex shape of the MHA inkwithin the molecular corral due to the different wetting properties ofthe gold substrate and hydrophobic corral. FIG. 21C: A molecularcross-shaped corral, where the horizontal lines are comprised of MHA andthe vertical lines are comprised of ODT. Note that the MHA, which isintroduced in the center of the corral, diffuses over the walls of thecorral comprised of MHA but remains confined within the walls comprisedof ODT. Also, note that the MI-IA structure within the corral assumes aconcave shape where the sidewalls are made of MHA (horizontal blackarrow) and a convex shape where the sidewalls are made of ODT (verticalblack arrow).

FIG. 22: Eight identical patterns generated with one imaging tip (whichuses a feedback system) and seven writing tips (passive; do not usefeedback systems separate from that of the imaging tip), all coated withODT molecules.

FIG. 23: A schematic representation of the DPN-based particleorganization strategy.

FIGS. 24A-C: Patterns generated on gold thin film by DPN, imaged bylateral force microscopy (MHA=light areas, ODT=dark areas). MHA dots[diameters 540 (FIG. 24A), 750 (FIG. 24B), and 240 nm (FIG. 24C),center-to-center distance 2 μm] deposited by holding the AFM tip at aseries of x,y coordinates (5, 10, and 15 seconds). Scale bars represent6 μm.

FIG. 25: Optical micrograph of particle arrays on a MHA-patternedsubstrate. Scale bar represents 20 μm.

FIG. 26: In situ optical micrograph of 1.0 μm diameter amine-modifiedpolystyrene particles organized into a square array with a latticeconstant of 2 μm. Note the dark fuzzy dots, which are particles insolution that have not reacted with the template (white arrows). Scalebar represents 6 μm.

FIGS. 27A-B: Two regions of a gold substrate with 190 nmamidine-modified polystyrene particles selectively organized on MHAregions of the patterned surface, imaged by intermittent-contact AFM.FIG. 27A—single particle array formed on 300 nm MHA dots. FIG. 27Bsingle particle array formed on 700 nm diameter MHA dots. Also, notethat the AFM tip in some case drags the particles from their preferredlocations.

FIG. 28A: Block diagram illustrating DPN software.

FIG. 28B: Flow chart illustrating pattern translator subroutine of DPNsoftware.

DETAILED DESCRIPTION OF THE PRESENTLY PREFERRED EMBODIMENTS

DPN utilizes a scanning probe microscope (SPM) tip. As used herein, thephrases “scanning probe microscope tip” and “SPM tip” are used to meantips used in atomic scale imaging, including atomic force microscope(AFM) tips, near field scanning optical microscope (NSOM) tips, scanningtunneling microscope (STM) tips, and devices having similar properties,including devices made especially for DPN using the guidelines providedherein. Many SPM tips are available commercially (e.g., from ParkScientific, Digital Instruments, Molecular Imaging, Nanonics Ltd. andTopometrix. Alternatively, SPM tips can be made by methods well known inthe art. For instance, SPM tips can be made by e-beam lithography (e.g.,a solid tip with a hole bored in it can be fabricated by e-beamlithography).

Most preferably, the SPM tip is an AFM tip. Any AFM tip can be used, andsuitable AFM tips include those that are available commercially from,e.g., Park Scientific, Digital Instruments and Molecular Imaging. Alsopreferred are NSOM tips usable in an AFM. These tips are hollow, and thepatterning compounds accumulate in the hollows of the NSOM tips whichserve as reservoirs of the patterning compound to produce a type of“fountain pen” for use in DPN. Suitable NSOM tips are available fromNanonics Ltd. and Topometrix. STM tips usable in an AFM are alsosuitable for DPN, and such tips can be fabricated (see, e.g. Giessibl etal., Science, 289, 422 (2000)) or can be obtained commercially (e.g.,from Thermomicroscopes, Digital Instruments, or Molecular Imaging).

The tip is also preferably one to which the patterning compoundphysisorbs only. As used herein “physisorb” means that the patterningcompound adheres to the tip surface by a means other than as a result ofa chemical reaction (i.e., no chemisorption or covalent linkage) and canbe removed from the tip surface with a suitable solvent. Physisorptionof the patterning compounds to the tip can be enhanced by coating thetip with an adhesion layer and by proper choice of solvent (when one isused) for the patterning compound. The adhesion layer is a uniform, thin(<10 nm) layer of material deposited on the tip surface which does notsignificantly change the tip's shape. It should also be strong enough totolerate AFM operation (force of about 10 nN). Titanium and chromiumform very thin uniform layers on tips without changing tip shapesignificantly, and are well-suited to be used to form the adhesionlayer. The tips can be coated with an adhesion layer by vacuumdeposition (see Holland, Vacuum Deposition Of Thin Films (Wiley, NewYork, N.Y., 1956)), or any other method of forming thin metal films. By“proper solvent” is meant a solvent that adheres to (wets) the tip well.The proper solvent will vary depending on the patterning compound used,the type of tip used, whether or not the tip is coated with an adhesionlayer, and the material used to form the adhesion layer. For example,acetonitrile adheres well to uncoated silicon nitride tips, making theuse of an adhesion layer unnecessary when acetonitriles used as thesolvent for a patterning compound. In contrast, water does not adhere touncoated silicon nitride tips. Water does adhere well to titanium-coatedsilicon nitride tips, and such coated tips can be used when water isused as the solvent. Physisorption of aqueous solutions of patterningcompounds can also be enhanced by increasing the hydrophilicity of thetips (whether coated or uncoated with an adhesion layer). For instance,hydrophilicity can be increased by cleaning the tips (e.g., with apiranha solution, by plasma cleaning, or with UV ozone cleaning) or byoxygen plasma etching. See Lo et al., Langmuir, 15, 6522-6526 (1999);James et al., Langmuir, 14, 741-744 (1998). Alternatively, a mixture ofwater and another solvent (e.g., 1:3 ratio of water:acetonitrile) mayadhere to uncoated silicon nitride tips, making the use of an adhesionlayer or treatment to increase hydrophilicity unnecessary. The propersolvent for a particular set of circumstances can be determinedempirically using the guidance provided herein.

The substrate may be of any shape and size. In particular, the substratemay be flat or curved. Substrates may be made of any material which canbe modified by a patterning compound to form stable surface structures(see below). Substrates useful in the practice of the invention includemetals (e.g., gold, silver, aluminum, copper, platinum, and paladium),metal oxides (e.g., oxides of Al, Ti, Fe, Ag, Zn, Zr, In, Sn and Cu),semiconductor materials (e.g., Si, CdSe, CdS and CdS coated with ZnS),magnetic materials (e.g., ferromagnetite), polymers or polymer-coatedsubstrates, superconductor materials (YBa₂Cu₃O_(7-δ)), Si, SiO₂, glass,AgI, AgBr, HgI₂, PbS, PbSe, ZnSe, ZnS, ZnTe, CdTe, InP, In₂O₃/SnO₂,In₂S₃, In₂Se₃, In₂Te₃, Cd₃P₂, Cd₃As_(2,) InAs, AlAs, GaP, and GaAs.Methods of making such substrates are well-known in the art and includeevaporation and sputtering (metal films), crystal semiconductor growth(e.g., Si, Ge, GaAs), chemical vapor deposition (semiconductor thinfilms), epitaxial growth (crystalline semiconductor thin films), andthermal shrinkage (oriented polymers). See, e.g., Alcock et al.,Canadian Metallurgical Quarterly, 23, 309 (1984); Holland, VacuumDeposition of Thin Films (Wiley, New York 1956); Grove, Philos. Trans.Faraday Soc., 87(1852); Teal, IEEE Trans. Electron Dev. ED-23,621(1976); Sell, Key Eng. Materials, 58, 169 (1991); Keller et al.,Float-Zone Silicon (Marcel Dekker, New York, 1981); Sherman, ChemicalVapor Deposition For Microelectronics: Principles, Technology AndApplications (Noyes, Park Ridges, N.J., 1987); Epitaxial SiliconTechnology (Baliga, ed., Academic Press, Orlando, Fla., 1986); U.S. Pat.No. 5,138,174; Hidber et al., Langmuir, 12, 5209-5215 (1996). Suitablesubstrates can also be obtained commercially from, e.g., DigitalInstruments (gold), Molecular Imaging (gold), Park Scientific (gold),Electronic Materials, Inc. (semiconductor wafers), Silicon Quest, Inc.(semiconductor wafers), MEMS Technology Applications Center, Inc.(semiconductor wafers), Crystal Specialties, Inc. (semiconductorwafers), Siltronix, Switzerland (silicon wafers), Aleene's, Buellton,Calif. (biaxially-oriented polystyrene sheets), and Kama Corp.,Hazelton, Pa. (oriented thin films of polystyrene).

The SPM tip is used to deliver a patterning compound to a substrate ofinterest. Any patterning compound can be used, provided it is capable ofmodifying the substrate to form stable surface structures. Stablesurface structures are formed by chemisorption of the molecules of thepatterning compound onto the substrate or by covalent linkage of themolecules of the patterning compound to the substrate.

Many suitable compounds which can be used as the patterning compound,and the corresponding substrate(s) for the compounds are known in theart. For example:

-   -   a. Compounds of the formula R₁SH, R₁SSR₂, R₁SR₂, R₁SO₂H, (R₁)₃P,        R₁NC, R₁CN, (R₁)₃N, R₁COOH, or ArSH can be used to pattern gold        substrates;    -   b. Compounds of formula R₁SH, (R₁)₃N, or ArSH can be used to        pattern silver, copper, palladium and semiconductor substrates;    -   c. Compounds of the formula R₁NC, R₁SH, R₁SSR₂, or R₁SR₂ can be        used to pattern platinum substrates;    -   d. Compounds of the formula R₁SH can be used to pattern        aluminum, TiO₂ SiO₂, GaAs and InP substrates;    -   e. Organosilanes, including compounds of the formula R₁SiCl₃,        R₁Si(OR₂)₃, (R₁COO)₂, R₁CH═CH₂, R₁Li or R₁MgX, can be used to        pattern Si, SiO₂ and glass substrates;    -   f. Compounds of the formula R₁COOH or R₁CONHR₂ can be used to        pattern metal oxide substrates;    -   g. Compounds of the formula R₁SH, R₁NH₂, ArNH₂ pyrrole, or        pyrrole derivatives wherein R₁ is attached to one of the carbons        of the pyrrole ring, can be used to pattern cuprate high        temperature superconductors;    -   h. Compounds of the formula R₁PO₃H₂ can be used to pattern ZrO₂        and In₂O₃/SnO₂ substrates;    -   i. Compounds of the formula R₁COOH can be used to pattern        aluminum, copper, silicon and platinum substrates;    -   j. Compounds that are unsaturated, such as azoalkanes (R₃NNR₃)        and isothiocyanates (R₃NCS), can be used to pattern silicon        substrates;    -   k. Proteins and peptides can be used to pattern, gold, silver,        glass, silicon, and polystyrene; and    -   l. Silazanes can be used to pattern SiO₂ and oxidized GaAs.        In the above formulas:    -   R₁ and R₂ each has the formula X(CH₂)n and, if a compound is        substituted with both R₁ and R₂, then R₁ and R₂ can be the same        or different;    -   R₃ has the formula CH₃(CH₂)n;    -   n is 0-30;    -   Ar is aryl;    -   X is —CH₃, —CHCH₃, COOH, CO₂(CH₂)_(m)CH₃, —OH, —CH₂OH, ethylene        glycol, hexa(ethylene glycol), —O(CH₂)_(m)CH₃, NH₂,        NH(CH₂)_(m)NH₂, halogen, glucose, maltose, fullerene C60, a        nucleic acid (oligonucleotide, DNA, RNA, etc.), a protein (e.g.,        an antibody or enzyme) or a ligand (e.g., an antigen, enzyme        substrate or receptor); and    -   m is 0-30.

For a description of patterning compounds and their preparation and use,see Xia and Whitesides, Angew. Chem. Int. Ed., 37, 550-575 (1998) andreferences cited therein; Bishop et al., Curr. Opinion Colloid &Interface Sci., 1, 127-136 (1996); Calvert, J. Vac. Sci. Technol. B, 11,2155-2163 (1993); Ulman, Chem. Rev., 96:1533 (1996) (alkanethiols ongold); Dubois et al., Annu. Rev. Phys. Chem., 43:437 (1992)(alkanethiols on gold); Ulman, An Introduction to Ultrathin OrganicFilms: From Langmuir-Blodgett to Self-Assembly (Academic, Boston, 1991)(alkanethiols on gold); Whitesides, Proceedings of the Robert A. WelchFoundation 39th Conference On Chemical Research Nanophase Chemistry,Houston, Tex., pages 109-121 (1995) (alkanethiols attached to gold);Mucic et al. Chem. Commun. 555-557 (1996) (describes a method ofattaching 3′ thiol DNA to gold surfaces); U.S. Pat. No. 5,472,881(binding of oligonucleotide-phosphorothiolates to gold surfaces);Burwell, Chemical Technology, 4, 370-377(1974) and Matteucci andCaruthers, J. Am. Chem. Soc., 103, 3185-3191 (1981) (binding ofoligonucleotide-alkylsiloxanes to silica and glass surfaces); Grabar etal., Anal. Chem., 67, 735-743 (binding of aminoalkylsiloxanes and forsimilar binding of mercaptoalkylsiloxanes); Nuzzo et al., J. Am. Chem.Soc., 109, 2358 (1987) (disulfides on gold); Allara and Nuzzo, Langmuir,1,45 (1985) (carboxylic acids on aluminum); Allara and Tompkins, J.Colloid Interface Sci., 49, 410-421(1974) (carboxylic acids on copper);Iler, The Chemistry Of Silica, Chapter 6, (Wiley 1979) (carboxylic acidson silica); Timmons and Zisman, J. Phys. Chem., 69, 984-990 (1965)(carboxylic acids on platinum); Soriaga and Hubbard, J. Am. Chem. Soc.,104, 3937 (1982) (aromatic ring compounds on platinum); Hubbard, Acc.Chem. Res., 13, 177 (1980) (sulfolanes, sulfoxides and otherfunctionalized solvents on platinum); Hickman et al., J. Am. Chem. Soc.,111, 7271 (1989) (isonitriles on platinum); Maoz and Sagiv, Langmuir, 3,1045 (1987) (silanes on silica); Maoz and Sagiv, Langmuir, 3, 1034(1987) (silanes on silica); Wasserman et al., Langmuir, 5, 1074(1989)(silanes on silica); Eltekova and Eltekov, Langmuir, 3, 951 (1987)(aromatic carboxylic acids, aldehydes, alcohols and methoxy groups ontitanium dioxide and silica); and Lec et al., J. Phys. Chem., 92, 2597(1988) (rigid phosphates on metals); Lo et al., J. Am. Chem. Soc., 118,11295-11296 (1996) (attachment of pyrroles to superconductors); Chen etal., J. Am. Chem. Soc., 117, 6374-5 (1995) (attachment of amines andthiols to superconductors); Chen et al., Langmuir, 12, 2622-2624 (1996)(attachment of thiols to superconductors); McDevitt et al., U.S. Pat.No. 5,846,909 (attachment of amines and thiols to superconductors); Xuet al., Langmuir, 14, 6505-6511 (1998) (attachment of amines tosuperconductors); Mirkin et al., Adv. Mater. (Weinheim, Ger.), 9,167-173 (1997) (attachment of amines to superconductors); Hovis et al.,J. Phys. Chem. B, 102, 6873-6879 (1998) (attachment of olefins anddienes to silicon); Hovis et al., Surf Sci., 402-404, 1-7 (1998)(attachment of olefins and dienes to silicon); Hovis et al., J. Phys.Chem. B, 101, 9581-9585 (1997) (attachment of olefins and dienes tosilicon); Hamers et al., J. Phys. Chem. B, 101, 1489-1492 (1997)(attachment of olefins and dienes to silicon); Hamers et al., U.S. Pat.No. 5,908,692 (attachment of olefins and dienes to silicon); Ellison etal., J. Phys. Chem. B, 103, 6243-6251 (1999) (attachment ofisothiocyanates to silicon); Ellison et al., J. Phys. Chem. B, 102,8510-8518 (1998) (attachment of azoalkanes to silicon); Ohno et al.,Mol. Cryst. Liq. Cryst. Sci. Technol., Sect. A, 295, 487-490 (1997)(attachment of thiols to GaAs); Reuter et al., Mater. Res. Soc. Symp.Proc., 380, 119-24 (1995) (attachment of thiols to GaAs); Bain, Adv.Mater. (Weinheim, Fed. Repub. Ger.), 4, 591-4 (1992) (attachment ofthiols to GaAs); Sheen et al., J. Am. Chem. Soc., 114, 1514-15 (1992)(attachment of thiols to GaAs); Nakagawa et al., Jpn. J. Appl. Phys.,Part 1, 30, 3759-62 (1991) (attachment of thiols to GaAs); Lunt et al.,J. Appl. Phys., 70, 7449-67 (1991) (attachment of thiols to GaAs); Luntet al., J. Vac. Sci. Technol., B, 9, 2333-6 (1991) (attachment of thiolsto GaAs); Yamamoto et al., Langmuir ACS ASAP, web release numberIa990467r (attachment of thiols to InP); Gu et al., J. Phys. Chem. B,102, 9015-9028(1998) (attachment of thiols to InP); Menzel et al., Adv.Mater. (Weinheim, Ger.), 11, 131-134 (1999) (attachment of disulfides togold); Yonezawa et al., Chem. Mater., 11, 33-35 (1999) (attachment ofdisulfides to gold); Porter et al., Langmuir, 14, 7378-7386 (1998)(attachment of disulfides to gold); Son et al., J. Phys. Chem., 98,8488-93 (1994) (attachment of nitrites to gold and silver); Steiner etal., Langmuir, 8, 2771-7 (1992) (attachment of nitrites to gold andcopper); Solomun et al., J. Phys. Chem., 95, 10041-9 (1991) (attachmentof nitrites to gold); Solomun et al. Ber. Bunsen-Ges. Phys. Chem.,95,95-8(1991) (attachment of nitriles to gold); Henderson et al., Inorg.Chim. Acta, 242, 115-24 (1996) (attachment of isonitriles to gold); Hucet al., J. Phys. Chem. B, 103, 10489-10495 (1999) (attachment ofisonitriles to gold); Hickman et al., Langmuir, 8, 357-9 (1992)(attachment of isonitriles to platinum); Steiner et al., Langmuir, 8,90-4 (1992) (attachment of amines and phosphines to gold and attachmentof amines to copper); Mayya et al., J. Phys. Chem. B, 101, 9790-9793(1997) (attachment of amines to gold and silver); Chen et al., Langmuir,15, 1075-1082 (1999) (attachment of carboxylates to gold); Tao, J. Am.Chem. Soc., 115, 4350-4358 (1993) (attachment of carboxylates to copperand silver); Laibinis et al., J. Am. Chem. Soc., 114, 1990-5 (1992)(attachment of thiols to silver and copper); Laibinis et al., Langmuir,7, 3167-73 (1991) (attachment of thiols to siher); Fenter et al.,Langmuir, 7, 2013-16 (1991) (attachment of thiols to silver); Chang etal., Am. Chem. Soc., 116, 6792-805 (1994) (attachment of thiols tosilver); Li et al., J. Phys. Chem., 98, 11751-5 (1994) (attachment ofthiols to silver); Li et al., Report, ²⁴pp (1994) (attachment of thiolsto silver); Tarlov et al., U.S. Pat. No. 5,942,397 (attachment of thiolsto silver and copper); Waldeck, et al., PCT application WO/99/48682(attachment of thiols to silver and copper); Gui et al., Langmuir, 7,955-63 (1991) (attachment of thiols to silver); Walczak et al., J. Am.Chem. Soc., 113, 2370-8(1991) (attachment of thiols to silver);Sangiorgi et al., Gazz. Chim. Ital., 111,99-102 (1981) (attachment ofamines to copper); Magallon et al., Book of Abstracts, 215th ACSNational Meeting, Dallas, Mar. 29-Apr. 2, 1998, COLL-048 (attachment ofamines to copper); Patil et al., Langmuir, 14,2707-2711 (1998)(attachment of amines to silver); Sastry et al., J. Phys. Chem. B, 101,4954-4958 (1997) (attachment of amines to silver); Bansal et al., J.Phys. Chem. B, 102, 4058-4060 (1998) (attachment of alkyl lithium tosilicon); Bansal et al., J. Phys. Chem. B, 102, 1067-1070 (1998)(attachment of alkyl lithium to silicon); Chidsey, Book of Abstracts,214th ACS National Meeting, Las Vegas, Nev. Sep. 7-11, 1997, I&EC-027(attachment of alkyl lithium to silicon); Song, J. H., Thesis,University of California at San Diego (1998) (attachment of alkyllithium to silicon dioxide); Meyer et al., J. Am. Chem. Soc., 110,4914-18 (1988) (attachment of amines to semiconductors); Brazdil et al.J. Phys. Chem., 85, 1005-14 (1981) (attachment of amines tosemiconductors); James et al., Langmuir, 14, 741-744 (1998) (attachmentof proteins and peptides to glass); Bernard et al., Langmuir, 14,2225-2229 (1998) (attachment of proteins to glass, polystyrene, gold,silver and silicon wafers); Pereira et al., J. Mater. Chem., 10, 259(2000) (attachment of silazanes to SiO₂); Pereira et al., J. Mater.Chem., 10, 259 (2000) (attachment of silazanes to SiO₂); Dammel,Diazonaphthoquinone Based Resists (1st ed., SPIE Optical EngineeringPress, Bellingham, Wash., 1993) (attachment of silazanes to SiO2);Anwander et al., J. Phys. Chem. B, 104, 3532 (2000) (attachment ofsilazanes to SiO₂); Slavov et al., J. Phys. Chem., 104, 983 (2000)(attachment of silazanes to SiO₂).

Other compounds known in the art besides those listed above, or whichare developed or discovered using the guidelines provided herein orotherwise, can also be used as the patterning compound. Presentlypreferred are alkanethiols and arylthiols on a variety of substrates andtrichlorosilanes on SiO₂ substrates (see Examples 1 and 2).

To practice DPN, the SPM tip is coated with a patterning compound. Thiscan be accomplished in a number of ways. For instance, the tip can becoated by vapor deposition, by direct contact scanning, or by bringingthe tip into contact with a solution of the patterning compound.

The simplest method of coating the tips is by direct contact scanning.Coating by direct contact scanning is accomplished by depositing a dropof a saturated solution of the patterning compound on a solid substrate(e.g., glass or silicon nitride; available from Fisher Scientific orMEMS Technology Application Center). Upon drying, the patterningcompound forms amicrocrystalline phase on the substrate. To coat thepatterning compound on the SPM tip, the tip is scanned repeatedly acrossthis microcrystalline phase. While this method is simple, it does notlead to the best loading of the tip, since it is difficult to controlthe amount of patterning compound transferred from the substrate to thetip.

The tips can also be coated by vapor deposition. See Sherman, ChemicalVapor Deposition For Microelectronics: Principles, Technology AndApplications (Noyes, Park Ridges, N.J., 1987). Briefly, a patterningcompound (in pure form, solid or liquid, no solvent) is placed on asolid substrate (e.g., glass or silicon nitride; obtained from FisherScientific or MEMS Technology Application Center), and the tip isposition near (within about 1-20 cm, depending on chamber design) thepatterning compound. The compound is then heated to a temperature atwhich it vaporizes, thereby coating the tip with the compound. Forinstance, 1-octadecanethiol can be vapor deposited at 60° C. Coating byvapor deposition should be performed in a closed chamber to preventcontamination of other areas. If the patterning compound is one which isoxidized by air, the chamber should be a vacuum chamber or anitrogen-filled chamber. Coating the tips by vapor deposition producesthin, uniform layers of patterning compounds on the tips and gives veryreliable results in DPN.

Preferably, however, the SPM tip is coated by dipping the tip into asolution of the patterning compound. The solvent is not critical; allthat is required is that the compound be in solution. However, thesolvent is preferably the one in which the patterning compound is mostsoluble. Also, the solution is preferably a saturated solution. Inaddition, the solvent is preferably one that adheres to (wets) the tip(uncoated or coated with an adhesion layer) very well (see above). Thetip is maintained in contact with the solution of the patterningcompound for a time sufficient for the compound to coat the tip. Suchtimes can be determined empirically. Generally, from about 30 seconds toabout 3 minutes is sufficient. Preferably, the tip is dipped in thesolution multiple times, with the tip being dried between each dipping.The number of times a tip needs to be dipped in a chosen solution can bedetermined empirically. Preferably, the tip is dried by blowing an inertgas (such as carbon tetrafluoride,1,2-dichloro-1,1,2,2,-tetrafluoroethane, dichlorodifluoromethane,octafluorocyclobutane, trichlorofluoromethane, difluoroethane, nitrogen,nitrogen, argon or dehumidified air) not containing any particles (i.e.,purified) over the tip. Generally, about 10 seconds of blowing with thegas at room temperature is sufficient to dry the tip. After dipping (thesingle dipping or the last of multiple dippings), the tip may be usedwet to pattern the substrate, or it may be dried (preferably asdescribed above) before use. A dry tip gives a low, but stable, rate oftransport of the patterning compound for a long time (on the order ofweeks), whereas a wet tip gives a high rate of transport of thepatterning compound for a short time (about 2-3 hours). A dry tip ispreferred for compounds having a good rate of transport under dryconditions (such as the compounds listed above wherein X═—CH₃), whereasa wet tip is preferred for compounds having a low rate of transportunder dry conditions (such as the compounds listed above whereinX═—COOH).

To perform DPN, the coated tip is used to apply a patterning compound toa substrate so as to form a desired pattern. The pattern may be anypattern and may be simple or complex. For instance, the pattern may be adot, a line, a cross, a geometric shape (e.g. a triangle, square orcircle), combinations of two or more of the foregoing, combinatorialarrays (e.g., a square array of rows and columns of dots), electroniccircuits, or part of, or a step in, the formation of a three-dimensionalstructure.

A transport medium is preferably used in DPN since, as presentlyunderstood, the patterning compound is transported to the substrate bycapillary transport. The transport medium forms a meniscus which bridgesthe gap between the tip and the substrate (see FIG. 1). Thus, the tip is“in contact” with the substrate when it is close enough so that thismeniscus forms. The tip may be actually touching the substrate, but itneed not be. The tip only needs to be close enough to the substrate sothat a meniscus forms. Suitable transport media include water,hydrocarbons (e.g., hexane), and solvents in which the patterningcompounds are soluble (e.g., the solvent used for coating the tip—seeabove). Faster writing with the tip can be accomplished by using thetransport medium in which the patterning compound is most soluble. Thepossibility that the patterning compound can be deposited on thesubstrate without the use of a transport medium has not been completelyruled out, although it seems highly unlikely. Even under conditions oflow, or even no humidity, there is likely some water on the substratewhich could function as the transport medium.

DPN is performed using an AFM or a device performing similar functionsand having similar properties, including devices developed especiallyfor performing DPN using the guidelines provided herein, usingtechniques that are conventional and well known in AFM microscopy.Briefly, the substrate is placed in the sample holder of the device, thesubstrate is contacted with the SPM tip(s) coated with the patterningcompound(s), and the substrate is scanned to pattern it with thepatterning compound(s). An AFM can be operated in several modes, and DPNcan be performed when the AFM or similar device is operated in any ofthese modes. For instance, DPN can be performed in (1) contact (constantforce) mode wherein the tip is maintained in contact with (touching) thesubstrate surface, (2) non-contact (dynamic) mode wherein the tip isvibrated very close to the substrate surface, and/or (3) intermittentcontact (tapping) mode which is very similar to the non-contact mode,except that the tip is allowed to strike (touch) the surface of thesubstrate.

Single tips can be to write a pattern utilizing an AFM or similardevice. Two or more different patterning compounds can be applied to thesame substrate to form patterns (the same or different) of the differentcompounds by: (1) removing a first tip coated with a first patterningcompound and replacing it with another tip coated with a differentpatterning compound; or (2) rinsing the first tip coated with the firstpatterning compound so as to remove the patterning compound from the tipand then coating the tip with a different patterning compound. Suitablesolvents for rinsing tips to remove patterning compounds are thosesolvents in which the patterning compound is soluble. Preferably, therinsing solvent is the solvent in which the patterning compound is mostsoluble. Rinsing of tips can be accomplished by simply dipping the tipin the rinsing solvent.

Alternatively, a plurality of tips can be used in a single AFM orsimilar device to write a plurality of patterns (the same pattern ordifferent patterns) on a substrate using the same or differentpatterning compounds (see, e.g., Example 6 below, U.S. Pat. Nos.5,630,923, and 5,666,190, Lutwyche et al., Sens. Actuators A, 73:89(1999), Vettiger et al., Microelectron Eng., 46:11(1999), Minne et al.,Appl. Phys. Lett., 73:1742 (1998), and Tsukamoto et al., Rev. Sci.Instrum., 62:1767 (1991) which describe devices comprising multiplecantilevers and tips for patterning a substrate). One or more of theplurality of tips can be rinsed as described above for single tips, ifdesired, to change the patterning compound coated on the tip(s).

The AFM or similar device used for DPN preferably comprises at least onemicron-scale well positioned so that the well(s) will be adjacent thesubstrate when the substrate is placed in the sample holder. Preferablythe AFM or similar device comprises a plurality of wells holding aplurality of patterning compounds or holding at least one patterningcompound and at least one rinsing solvent. ¢Well” is used herein to meanany container, device, or material that can hold a patterning compoundor rinsing solvent and includes depressions, channels and other wellswhich can be prepared by microfabrication (e.g, the same processes usedto fabricate microelectronic devices, such as photolithograpy; see,e.g., PCT application WO 00/04390). The wells may also simply be piecesof filter paper soaked in a patterning compound or rinsing solvent. Thewells can be mounted anywhere on the AFM or similar device which isadjacent the substrate and whereby they can be addressed by the SPMtip(s), such as on the sample holder or translation stage.

When two or more patterns and/or two or more patterning compounds (inthe same or different patterns) are applied to a single substrate, apositioning (registration) system is used to align the patterns and/orpatterning compounds relative to each other and/or relative to selectedalignment marks. For instance, two or more alignment marks, which can beimaged by normal AFM imaging methods, are applied to the substrate byDPN or another lithographic technique (such as photolithography ore-beam lithography). The alignment marks may be simple shapes, such as across or rectangle. Better resolution is obtained by making thealignment marks using DPN. If DPN is used, the alignment marks arepreferably made with patterning compounds which form strong covalentbonds with the substrate. The best compound for forming the alignmentmarks on gold substrates is 16-mercaptohexadecanoic acid. The alignmentmarks are imaged by normal AFM methods (such as lateral force AFMimaging, AFM topography imaging and non-contact mode AFM imaging),preferably using an SPM tip coated with a patterning compound for makinga desired pattern. For this reason, the patterning compounds used tomake the alignment marks should not react with the other patterningcompounds which are to be used to make the desired patterns and shouldnot be destroyed by subsequent DPN patterning. Using the imaging data,the proper parameters (position and orientation) can be calculated usingsimple computer programs (e.g., Microsoft Excel spreadsheet), and thedesired pattern(s) deposited on the substrate using the calculatedparameters. Virtually an infinite number of patterns and/or patterningcompounds can be positioned using the alignment marks since the systemis based on calculating positions and orientations relative to thealignment marks. To get the best results, the SPM tip positioning systemwhich is used should be stable and not have drift problems. One AFMpositioning system which meets these standards is the 100 micrometerpizoelectric tube scanner available from Park Scientific. It providesstable positioning with nanometer scale resolution.

DPN can also be used in a nanoplotter format by having a series of wellscontaining a plurality of different patterning compounds and rinsingsolvents adjacent the substrate. One or more tips can be used. When aplurality of tips is used, the tips can be used serially or in parallelto produce patterns on the substrate.

In a nanoplotter format using a single tip, the tip is dipped into awell containing a patterning compound to coat the tip, and the coatedtip is used to apply a pattern to the substrate. The tip is then rinsedby dipping it in a well containing a rinsing solvent or a series of suchwells. The rinsed tip is then dipped into another well to be coated witha second patterning compound and is used to apply a pattern to thesubstrate with the second patterning compound. The patterns are alignedas described in the previous paragraph. The process of coating the tipwith patterning compounds, applying a pattern to the substrate, andrinsing the tip, can be repeated as many times as desired, and theentire process can be automated using appropriate software.

A particularly preferred nanoplotter format is described in Example 6and illustrated in FIGS. 17 and 18. In this preferred format, aplurality of AFM tips are attached to an AFM. A multiple-tip array canbe fabricated by simply physically separating an array of the desirednumber of cantilevers from a commercially-available wafer blockcontaining a large number of individual cantilevers, and this array canbe used as a single cantilever on the AFM. The array can be attached tothe AFM tip holder in a variety of ways, e.g. with epoxy glue. Ofcourse, arrays of tips of any spacing or configuration and adapted forattachment to an AFM tip holder can be microfabricated by methods knownin the art. See, e.g., Minne et al., Applied Physics Letters, 72:2340(1998). The plurality of tips in the array can be employed for serial orparallel DPN. When the plurality of tips is used for parallel DPN, onlyone of the tips needs to be connected to a feedback system (this tip isreferred to as the “imaging tip”). The feedback system is a standardfeedback system for an AFM and comprises a laser, photodiode andfeedback electronics. The remaining tips (referred to as “writing tips”)are guided by the imaging tip (i.e., all of the writing tips reproducewhat occurs at the imaging tip in passive fashion). As a consequence,all of the writing tips will produce the same pattern on the substrateas produced by the imaging tip. Of course, each writing tip may becoated with a patterning compound which is the same or different thanthat coated on the imaging tip or on the other writing tips, so that thesame pattern is produced using the same patterning compound or usingdifferent patterning compounds. When serial DPN is employed, each of thetips used in sequence must be connected to a feedback system(simultaneously or sequentially). The only adaptation of the AFMnecessary to provide for a choice of serial or parallel DPN is to add atilt stage to the AFM. The tilt stage is adapted for receiving andholding the sample holder, which in turn is adapted for receiving andholding the substrate. Tilt stages are included with many AFM's or canbe obtained commercially (e.g., from Newport Corp.) and attached to theAFM according to the manufacturer's instructions. The AFM preferablyalso comprises a plurality of wells located adjacent the substrate andso that the AFM operator can individually address and coat the tips withpatterning compounds or rinse the tips with rinsing solvents. Some AFM'sare equipped with a translation stage which can move very largedistances (e.g., the M5 AFM from Thermomicroscopes), and the wells canbe mounted on this type of translation stage. For inking or rinsing, awell is moved below an AFM tip by the translation stage and, then, thetip is lowered by a standard coarse approach motor until it touches theink or solvent in the well. The tip is held in contact with the ink orsolvent in order to coat or rinse the tip. The wells could also bemounted on the sample holder or tilt stage.

DPN can also be used to apply a second patterning compound to a firstpatterning compound which has already been applied to a substrate. Thefirst patterning compound can be applied to the substrate by DPN,microcontact printing (see, e.g, Xia and Whitesides, Angew. Chem. IndEd., 37, 550-575 (1998); James et al., Langmuir, 14, 741-744 (1998);Bernard et al., Langmuir, 14, 2225-2229 (1998); Huck et al., Langmuir,15, 6862-6867 (1999)), by self-assembly of a monolayer on a substrateimmersed in the compound (see, e.g. Ross et al., Langmuir, 9, 632-636(1993); Bishop and Nuzzo, Curr. Opinion in Colloid & Interface Science,1, 127-136 (1996); Xia and Whitesides, Angew. Chem. Ind. Ed., 37,550-575 (1998);Yan et al., Langmuir, 15, 1208-1214 (1999); Lahiri etal., Langmuir, 15, 2055-2060 (1999); Huck et al., Langmuir, 15,6862-6867 (1999)), or any other method. The second patterning compoundis chosen so that it reacts chemically or otherwise stably combines(e.g., by hybridization of two complimentary strands of nucleic acid)with the first patterning compound. See, e.g., Dubois and Nuzzo, Annu.Rev. Phys. Chem., 43, 437-63 (1992); Yan et al., Langmuir, 15, 1208-1214(1999); Lahiri et al., Langmuir, 15, 2055-2060 (1999); and Huck et al.,Langmuir, 15, 6862-6867 (1999). As with DPN performed directly on asubstrate, both the second patterning compound and a transport mediumare necessary, since the second patterning compound is transported tothe first patterning compound by capillary transport (see above). Third,fourth, etc., patterning compounds can also be applied to the firstpatterning compound, or to other patterning compounds, already on thesubstrate. Further, additional patterning compounds can be applied toform multiple layers of patterning compounds. Each of these additionalpatterning compounds may be the same or different than the otherpatterning compounds, and each of the multiple layers may be the same ordifferent than the other layers and may be composed of one or moredifferent patterning compounds.

Further, DPN can be used in combination with other lithographictechniques. For instance, DPN can be used in conjunction withmicrocontact printing and the other lithographic techniques discussed inthe Background section above.

DPN can also be used in conjunction with wet (chemical) etchingtechniques. In particular, an SPM tip can be used to deliver apatterning compound to a substrate of interest in a pattern of interest,all as described above, and the patterning compound functions as anetching resist in one or more subsequent wet etching procedures. Thepatterning compounds can be used to pattern the substrate prior to anyetching or after one or more etching steps have been performed toprotect areas exposed by the etching step(s). The wet etching proceduresand materials used in them are standard and well known in the art. See,e.g., Xia et al., Angew. Chem. Int. Ed., 37, 550 (1998); Xia et al.,Chem. Mater., 7, 2332 (1995); Kumar et al., J. Am. Chem. Soc., 114,9188-9189 (1992); Seidel et al., J. Electrochem. Soc., 137, 3612 (1990).Wet etching procedures are used for, e.g., the preparation ofthree-dimensional architectures on or in substrates (e.g., Si wafers) ofinterest. See, e.g., Xia et al., Angew. Chem. Int. Ed, 37, 550 (1998);Xia et al., Chem. Mater., 7, 2332 (1995). After etching, the patterningcompound may be retained on the substrate or removed from it. Methods ofremoving the patterning compounds from the substrates are well known inthe art. See, e.g., Example 5.

Several parameters affect the resolution of DPN, and its ultimateresolution is not yet clear. First, the grain size of the substrateaffects DPN resolution much like the texture of paper controls theresolution of conventional writing. As shown in Example 1 below, DPN hasbeen used to make lines 30 nm in width on a particular gold substrate.This size is the average grain diameter of the gold substrate, and itrepresents the resolution limit of DPN on this type of substrate: It isexpected that better resolution will be obtained using smoother (smallergrain size) substrates, such as silicon. Indeed, using another, smoothergold substrate, the resolution was increased to 15 nm (see Example 4).

Second, chemisorption, covalent attachment and self-assembly all act tolimit diffusion of the molecules after deposition. In contrast,compounds, such as water, which do not anchor to the substrate, formonly metastable patterns of poor resolution (See Piner et al., Langmuir,13:6864 (1997)) and cannot be used.

Third, the tip-substrate contact time and, thus, scan speed influenceDPN resolution. Faster scan speeds and a smaller number of traces givenarrower lines.

Fourth, the rate of transport of the patterning compound from the tip tothe substrate affects resolution. For instance, using water as thetransport medium, it has been found that relative humidity affects theresolution of the lithographic process. For example, a 30-nm-wide line(FIG. 2C) required 5 minutes to generate in a 34% relative humidityenvironment, whereas a 100-nm-line (FIG. 2D) required 1.5 minutes togenerate in a 42% relative humidity environment. It is known that thesize of the water meniscus that bridges the tip and substrate dependsupon relative humidity (Piner et al., Langmuir, 13:6864 (1997)), and thesize of the water meniscus affects the rate of transport of thepatterning compound to the substrate. Further, when a wet tip is used,the water meniscus contains residual solvent is the transport medium,and the transport rate is also affected by the properties of thesolvent.

Fifth, the sharpness of the tip also affects the resolution of DPN.Thus, it is expected that better resolution will be obtained usingsharper tips (e.g., by changing the tips frequently, cleaning the tipsbefore coating them, and attaching sharp structures (such as carbonnanotubes) to the ends of the tips).

In summary, DPN is a simple but powerful method for transportingmolecules from SPM tips to substrates at resolutions comparable to thoseachieved with much more expensive and sophisticated competitivelithographic methods, such as electron-beam lithography. DPN is a usefultool for creating and functionalizing microscale and nanoscalestructures. For instance, DPN can be used in the fabrication ofmicrosensors, microreactors, combinatorial arrays, micromechanicalsystems, microarialytical systems, biosurfaces, biomaterials,microelectronics, microoptical systems, and nanoelectronic devices. See,e.g., Xia and Whitesides, Angew. Chem. Int. Ed., 37,550-575 (1998). DPNshould be especially useful for the detailed functionalization ofnanoscale devices prepared by more-conventional lithographic methods.See Reed et al., Science, 278:252 (1997); Feldheim et al., Chem. Soc.Rev., 27:1 (1998).

DPN, particularly parallel DPN, should also be especially useful for thepreparation of arrays, particular combinatorial arrays. An “array” is anarrangement of a plurality of discrete sample areas in a pattern on asubstrate. The sample areas may be any shape (e.g., dots, circles,squares or triangles) and maybe arranged in any pattern (e.g., rows andcolumns of discrete sample areas). Each sample area may contain the sameor a different sample as contained in the other sample areas of thearray. A “combinatorial array” is an array wherein each sample area or asmall group of replicate sample areas (usually 2-4) contain(s) a samplewhich is different than that found in other sample areas of the array. A“sample” is a material or combination of materials to be studied,identified, reacted, etc.

DPN will be particularly useful for the preparation of combinatorialarrays on the submicrometer scale. An “array on the submicrometer scale”means that at least one of the dimensions (e.g, length, width ordiameter) of the sample areas, excluding the depth, is less than 1 μm.At present, DPN can be used to prepare dots that are 10 nm in diameter.With improvements in tips (e.g., sharper tips), it should be possible toproduce dots that approach 1 nm in diameter. Arrays on a submicrometerscale allow for faster reaction times and the use of less reagents thanthe currently-used microscale (i.e., having dimensions, other thandepth, which are 1-999 μm) and larger arrays. Also, more information canbe gained per unit area (i.e., the arrays are more dense than thecurrently-used micrometer scale arrays). Finally, the use ofsubmicrometer arrays provides new opportunities for screening. Forinstance, such arrays can be screened with SPM's to look for physicalchanges in the patterns (e.g., shape, stickiness, height) and/or toidentify chemicals present in the sample areas, including sequencing ofnucleic acids (see below).

Each sample area of an array contains a single sample. For instance, thesample may be a biological material, such as a nucleic acid (e.g., anoligonucleotide, DNA, or RNA), protein or peptide (e.g., an antibody oran enzyme), ligand (e.g., an antigen, enzyme substrate, receptor or theligand for a receptor), or a combination or mixture of biologicalmaterials (e.g., a mixture of proteins). Such materials may be depositeddirectly on a desired substrate as described above (see the descriptionof patterning compounds above). Alternatively, each sample area maycontain a compound for capturing the biological material. See, e.g. PCTapplications WO 00/04382, WO 00/04389 and WO 00/04390, the completedisclosures of which are incorporated herein-by reference. For instance,patterning compounds terminating in certain functional groups (e.g.,—COOH) can bind proteins through a functional group present on, or addedto, the protein (e.g., —NH₂). Also, it has been reported thatpolylysine, which can be attached to the substrate as described above,promotes the binding cells to substrates. See James et al., Langmuir,14, 741-744 (1998). As another example, each sample area may contain achemical compound (organic, inorganic and composite materials) or amixture of chemical compounds. Chemical compounds may be depositeddirectly on the substrate or may be attached through a functional grouppresent on a patterning compound present in the sample area. As yetanother example, each sample area may contain a type of microparticlesor nanoparticles. See Example 7. From the foregoing, those skilled inthe art will recognize that a patterning compound may comprise a sampleor may be used to capture a sample.

Arrays and methods of using them are known in the art. For instance,such arrays can be used for biological and chemical screenings toidentify and/or quantitate a biological or chemical material (e.g.,immunoassays, enzyme activity assays, genomics, and proteomics).Biological and chemical libraries of naturally-occurring or syntheticcompounds and other materials, including cells, can be used, e.g., toidentify and design or refine drug candidates, enzyme inhibitors,ligands for receptors, and receptors for ligands, and in genomics andproteomics. Arrays of microparticles and nanoparticles can be used for avariety of purposes (see Example 7). Arrays can also be used for studiesof crystallization, etching (see Example 5), etc. References describingcombinatorial arrays and other arrays and their uses include U.S. Pat.Nos. 5,747,334, 5,962,736, and 5,985,356, and PCT applications WO96/31625, WO 99/31267, WO 00/04382, WO 00/04389, WO 00/04390, WO 00/36136, and WO 00/46406.

Results of experiments performed on the arrays of the invention can bedetected by conventional means (e.g., fluorescence, chemiluminescence,bioluminescence, and radioactivity). Alternatively, an SPM can be usedfor screening arrays. For instance, an AFM can be used for quantitativeimaging and identification of molecules, including the imaging andidentification of chemical and biological molecules through the use ofan SPM tip coated with a chemical or biomolecular identifier. SeeFrisbie et al., Science, 265,2071 2074 (1994); Wilbur et al., Langmuir,11, 825-831 (1995); Noy et al., J. Am. Chem. Soc., 117, 7943-7951(1995);Noy et al., Langmuir, 14, 1508-1511 (1998); and U.S. Pat. Nos.5,363,697, 5,372,93, 5,472,881 and 5,874,668, the complete disclosuresof which are incorporated herein by reference.

The present invention also includes novel components for more preciselydepositing patterns on a substrate by DPN. In particular, the presentinvention includes a component that receives as input dot sizes and linewidths of the patterning compound to be deposited on the substrate, andsubsequently determines the corresponding parameter values that can beused in controlling the lower level software and hardware that depositsthe substance on the substrate, e.g., such lower level software andhardware includes AFM systems. That is, since such lower level softwareand hardware (also denoted herein as AFM software and AFM hardware)typically are controlled by inputs such as “holding time” orstationarily depositing a dot of a desired size (e.g., diameter), and/orsubstrate drawing speed for depositing a line having a desired linewidth, the present invention includes a component for translatingbetween: (a) dot size and line width, and (b) holding time and drawingspeed, respectively. Moreover, since it is has been determined that dotsize and line width are each a function of the diffusion rate of thepatterning compound onto the- substrate, the component for translating(also denoted a “pattern translator” or merely “translator” herein)translates between (a) and (b) above by using such diffusion rates. Inparticular, the applicants have determined that:

-   -   (i) dot size may be determined according to the following        equation:        R={square root}{square root over (C*t/π)},        where R is the radius of the dot, t is the holding time, and C        is the diffusion constant, wherein C is, in turn, determined by        the tip characteristics, the substrate, the patterning compound,        and the contact force of the tip against the substrate; and    -   (ii) line width may be determined according to the following        equation:        W=C/s,        wherein W is the line width, s is the tip sweeping (e.g.,        drawing) speed, and C is as described above

To more fully describe the components for performing the precision DPNof the present invention, reference is made to FIG. 28A which is a highlevel diagram of the DPN system 2004 of the present invention.Accordingly, this system includes a DPN geometry engine 2008 whichprovides a user interactive DNP application software components forallowing a user to interactively design DPN patterns. In one embodiment,the DNP application components are provided on a WINDOWS 2000 platformby Microsoft Corp. More specifically, the DPN geometry engine 2008includes the following modules:

To more fully describe the components for performing the precision DPNof the present invention, reference is made to FIG. 28A which is a highlevel diagram of the DPN system 2004 of the present invention.Accordingly, this system includes a DPN geometry engine 2008 whichprovides a user interactive DNP application software components forallowing a user to interactively design DPN patterns. In one embodiment,the DNP application components are provided on a WINDOWS 2000 platformby Microsoft Corp. More specifically, the DPN geometry engine 2008includes the following modules:

-   -   (a) A computer aided design system 2012 (CAD) for generating at        least two dimensional patterns.    -   (b) A user interface 2016 for interacting with the computer        aided design system, and for supplying information related        specifically to the DPN process to be performed, such as, the        identifications of the substrate, and the patterning compound to        be deposited. Additionally, a user may be able to input tip        characteristics such as tip shape, and tip materials, as well as        an expected tip contact force against substrate. Note that the        user interface 2016 may provide graphical presentations to the        user's display 2020. Alternatively, the user interface may        receive input from a non-interactive source such a networked        database (not shown). In one embodiment, the user may have        multiple concurrent window presentations of his/her pattern or        design.    -   (c) A DPN runtime parameter storage 2024 for storing the DPN        specific parameters such as the identification of the substrate        and patterning compound, the tip characteristics, and contact        force as in (b) immediately above.

Patterns are output from the CAD 2012 to the pattern translator 2028 fortranslating into specifications of dots and piecewise linear shapes thatcan then be output to the drawing system 2030 which, e.g., may be anatomic force microscope system. In particular, this output is providedto the AFM software drivers 2032, wherein as mentioned above thesedrivers accept commands having values of holding time and drawing speedrather than dot size and line width. Additionally, the patterntranslator 2028 also receives input from the DPN runtime parameterstorage 2024 providing the parameter values identified in (c) above.Note that upon receiving the inputs from the CAD 2012 and the parameterstorage 2024, the pattern translator 2028 may query a diffusioncalibration database/expert system 2036 for the diffusion constant(s) Cas described hereinabove. That is, the pattern translator 2028 uses theparameter values obtained from the parameter storage 2024 to query thediffusion calibration database/expert system 2036 for the correspondingdiffusion constant(s) C that are to be applied to corresponding inputfrom the CAD 2012. Subsequently, the pattern translator 2028 generatesAFM commands for output to the AFM software drivers 2032, wherein eachof the AFM commands is typically one of the following tip movementcommands:

-   -   (a) Keep the tip away from the substrate surface.    -   (b) Hold the tip in contact with the substrate surface at a        fixed position for a given time (t) with a given force.    -   (c) Move the tip, while in contact with the substrate, in a line        from a first point to a second point at a given (fixed or        variable) speed.

Subsequently, the AFM software drivers 2032 direct the AFM hardware 2040to apply the patterning compound to the substrate according to thecommands received by the AFM software drivers 2032. Note that, for atleast some of the AFM commands, the corresponding tip movement is in arange of approximately one nanometer to one hundred micrometers.However, dots provided by the present invention may be approximately onenanometer. Moreover, it is within the scope of the present inventionthat the AFM software drivers 2032 and the AFM hardware 2040 may utilizemultiple drawing tips for drawing on the substrate. In particular, eachdrawing tip may use a different patterning compound (e.g., differentink). Note that the AFM software drivers 2032 may generate the tipcontrols for which of the multiple tips to use at any given time duringa drawing of a pattern by the drawing system 2030.

Note that the AFM software drivers 2032 can be commercially obtainedfrom Thermomicroscopes, 9830 S. 51st Street, Suite A 124 Phoenix, Ariz.85044. Additionally, the AFM hardware can be obtained fromThermomicroscopes or one or more of the following companies: Veeco_Inc.,112 Robin Hill Road, Santa Barbara, Calif. 93117, or Molecular ImagingInc., 1171 Borregas Avenue, Sunnyvale, Calif. 94089.

Additionally, note in an alternative embodiment, the diffusion rates maybe empirically determined by the user, and accordingly, the diffusioncalibration database/expert system 2036 maybe unnecessary. Instead theuser may enter the diffusion rates, e.g., via the user interface 2016.

In FIG. 28B a high level flowchart is provided of the steps performed bythe pattern translator 2028. In step 2054, the pattern translator 2028receives a design (CAD) file from the CAD 2012. In step 2058, thepattern translator 2028 retrieves all corresponding DPN parameters forthe DPN runtime parameter storage 2024. Note that, in one embodiment,there may be different such parameter values for different geometricdata entities in the CAD file. Additionally, note that in anotherembodiment, the DPN parameter values may be provided in the CAD file andassociated with their corresponding geometric entities. Further, in asimple case where such DPN parameter values are the same for allgeometric entities, the DPN parameter values may occur in the CAD fileonly once wherein this occurrence is applicable to all geometricentities therein. Following this, in step 2062, a first geometric entityin the design file is obtained (denoted herein as “G”). Thus, in step2066, the corresponding DPN parameter values are determined for G.Subsequently, in step 2070, the diffusion constant, C₀, is obtained fromthe diffusion calibration database/expert system 2036. Note that as thisdatabase's name implies, it may be substantially a database (e.g., arelational database) that contains, e.g., a table associating a dotsize, a patterning compound, a substrate, tip characteristics, and acontact force with a desired holding time for obtaining the dot size forthe patterning compound on the substrate when the tip has the tipcharacteristics and the tip contacts the substrate surface with thecontact force. Similarly, such a database will have a table associatinga line width, a patterning compound, a substrate, tip characteristics,and a contact force with a desired holding time for obtaining the linewidth for a line of the patterning compound on the substrate when thetip has the tip characteristics and the tip contacts the substratesurface with the contact force. For example, the following is anillustration of entries in such a table: Patterning Sub- ContactDiffusion Compounds strate Tip force constant 1-octadecanethiol goldMicro- 1 nano 0.08 mm²/sec lever A newton 16-mercaptohexadecanoic goldMicro- 1 nano 0.04 mm²/sec acid lever A newton Silazane gold Micro- 1nano 0.05 mm²/sec lever A newton Silazane gold Micro- 1 nano 0.03mm²/sec lever A newton

Note, however, in some embodiments, such tables may be very large and/ornot all combinations will have been previously determined (i.e.,calibrated). Accordingly, where the invention embodiment is used with,e.g., various combinations of patterning compounds (e.g., differentinks, or etching mask substances), and/or on various substrates, and/orwhere various types of tips may be used, the diffusion calibrationdatabase/expert system 2036 may intelligently compute, infer orinterpolate a likely holding time and/or drawing speed. For example, arule based expert system may be one embodiment of the diffusioncalibration database/expert system 2036 for determining a likelydiffusion constant. Additionally, note that when such a new a dot sizeand/or line width is verified for a particular patterning compound,substrate, tip characteristics, and contact force, then such values maybe associated and stored for subsequent use by the diffusion calibrationdatabase/expert system 2036.

In another alternative embodiment, instead of storing the diffusionconstant, the holding times and drawing speeds may be associated withdot size and line width as well as the patterning compound, substrate,tip characteristics, and contact force.

Referring again to FIG. 28B, in step 2074, the diffusion constant Co isused to determine a corresponding holding time and/or drawing speed for,respectively, each dot and piecewise linear portion of G. Thus, in step2078, the pattern translator 2028 generates the AFM commands for drawingeach portion of G and writes the generated AFM commands to an outputfile. Note, the software for generating sequences of AFM commands fordrawing geometric entities is known to those skilled in the art, andsuch software is used in, e.g., dot matrix printers. Consequently, instep 2082, a determination is made as to whether there are additionalgeometric entities in the CAD file that need to be translated into AFMdrawing commands. If so, then step 2062 is again encountered.Alternatively, step 2086 is performed, wherein the output file of AFMcommands is provided as input to the AFM software drivers 2032.

Note that further details regarding the pattern translator 2020 areprovided in the APPENDIX hereinbelow.

The invention also provides kits for performing DPN. In one embodiment,the kit comprises a container holding a patterning compound andinstructions directing that the patterning compound be used to coat ascanning probe microscope tip and that the coated tip should be used toapply the patterning compound to the substrate so as to produce adesired pattern. This kit may further comprise a container holding arinsing solvent, a scanning probe microscope tip a substrate, orcombinations thereof. In another embodiment, the kit comprises ascanning probe microscope tip coated with a patterning compound. Thiskit may further comprise a substrate, one or more containers, eachholding a patterning compound or a rinsing solvent, or both. Thesubstrates, tips, patterning compounds, and rinsing solvents are thosedescribed above. Any suitable container can be used, such as a vial,tube, jar, or a well or an array of wells. The kit may further comprisematerials for forming a thin solid adhesion layer to enhancephysisorption of the patterning compounds to the tips as described above(such as a container of titanium or chromium), materials useful forcoating the tips with the patterning compounds (such as solvents for thepatterning compounds or solid substrates for direct contact scanning),materials for performing lithography by methods other than DPN (see theBackground section and references cited therein), and/or materials forwet etching. Finally, the kit may comprise other reagents and itemsuseful for performing DPN or any other lithography method, such asreagents, beakers, vials, etc.

The invention further provides an AFM adapted for performing DPN. In oneembodiment, this microscope comprises a sample holder adapted forreceiving and holding a substrate and at least one well holding apatterning compound, the well being positioned so that it will beadjacent the substrate when the substrate is placed in the sample holderand and so that it can be addressed by an SPM tip mounted on the AFM.The sample holder, wells and tips are described above. In anotherembodiment, the microscope comprises a plurality of scanning probemicroscope tips and a tilt stage adapted for receiving and holding asample holder, the sample holder being adapted for receiving and holdinga substrate. The plurality of scanning pr e microscope tips and the tiltstage are described above.

As noted above, when an AFM is operated in air, water condenses betweenthe tip and surface and then is transported by means of the capillary asthe tip is scanned across the surface. This filled capillary, and thecapillary force associated with it, significantly impede the operationof the AFM and substantially affect the imaging process.

Quite surprisingly, it has been found that AFM tips coated with certainhydrophobic compounds exhibit an improved ability to image substrates inair by AFM as compared to uncoated tips. The reason for this is that thehydrophobic molecules reduce the size of the water meniscus formed andeffectively reduce friction. As a consequence, the resolution of AFM inair is increased using a coated tip, as compared to using an uncoatedtip. Accordingly, coating tips with the hydrophobic molecules can beutilized as a general pretreatment for AFM tips for performing AFM inair.

Hydrophobic compounds useful for coating AFM tips for performing AFM inair must form a uniform thin coating on the tip surface, must not bindcovalently to the substrate being imaged or to the tip, must bind to thetip more strongly than to the substrate, and must stay solid at thetemperature of AFM operation. Suitable hydrophobic compounds includethose hydrophobic compounds described above for use as patterningcompounds, provided that such hydrophobic patterning compounds are notused to coat AFM tips which are used to image a corresponding substratefor the patterning compound or to coat AFM tips which are made of, orcoated with, materials useful as the corresponding substrate for thepatterning compound. Preferred hydrophobic compounds for most substratesare those having the formula R₄NH₂, wherein R₄ is an alkyl of theformula CH₃(CN₂) or an aryl, and n is 0-30, preferably 10-20 (seediscussion of patterning compounds above). Particularly preferred is1-dodecylamine for AFM temperatures of operation below 74° F. (about23.3° C.).

AFM in air using any AFM tip may be improved by coating the AFM tip withthe hydrophobic compounds described in the previous paragraph. SuitableAFM tips include those described above for use in DPN.

AFM tips can be coated with the hydrophobic compounds in a variety ofways. Suitable methods include those described above for coating AFMtips with patterning compounds for use in DPN. Preferably, the AFM tipis coated with a hydrophobic compound by simply dipping the tip into asolution of the compound for a sufficient time to coat the tip and thendrying the coated tip with an inert gas, all as described above forcoating a tip with a patterning compound.

After the tip is coated, AFM is performed in the same manner as it wouldbe if the tip were not coated. No changes in AFM procedures have beenfound necessary.

EXAMPLES Example 1 “Dip Pen” Nanolithography with Alkanethiols on a GoldSubstrate

The transfer of 1-octadecanethiol (ODT) to gold (Au) surfaces is asystem that has been studied extensively. See Bain et al., Angew. Chem.Int. Ed. Engl, 28:506 (1989); A. Ulman, An Introduction to UltrathinOrganic Films: From Langmuir-Blodgett to Self-Assembly (Academic Press,Boston, 1991); Dubois et al., Annu. Rev. Phys. Chem., 43 :437 (1992);Bishop et al., Curr. Opin. Coll. Interf. Sci., 1:127(1996); Alves etal., J. Am. Chem. Soc., 114:1222(1992). Au having thismoderately-air-stable molecule immobilized on it can be easilydifferentiated from unmodified Au by means of lateral force microscopy(LFM).

When an AFM tip coated with ODT is brought into contact with a samplesurface, the ODT flows from the tip to the sample by capillary action,much like a dip pen (FIG. 1). This process has been studied using aconventional AFM tip on thin film substrates that were prepared bythermally evaporating 300 Å of polycrystalline Au onto mica at roomtemperature. A Park Scientific Model CP AFM instrument was used toperform all experiments. The scanner was enclosed in a glass isolationchamber, and the relative humidity was measured with a hygrometer. Allhumidity measurements have an absolute error of ±5%. A silicon nitridetip (Park Scientific, Microlever A) was coated with ODT by dipping thecantilever into a saturated solution of ODT in acetonitrile for 1minute. The cantilever was blown dry with compressed difluoroethaneprior to use.

A simple demonstration of the DPN process involved raster scanning a tipthat was prepared in this manner across a 1 μm by 1 μm section of a Ausubstrate (FIG. 2A). An LFM image of this section within a larger scanarea (3 μm by 3 μm) showed two areas of differing contrast (FIG. 2A).The interior dark area, or region of lower lateral force, was adeposited monolayer of ODT, and the exterior lighter area was bare Au.

Formation of high-quality self-assembled monolayers (SAMs) occurred whenthe deposition process was carried out on Au(111)/mica, which wasprepared by annealing the Au thin film substrates at 300° C. for 3hours. Alves et al., J Am. Chem. Soc., 114:1222 (1992). In this case, itwas possible to obtain a lattice-resolved image of an ODT SAM (FIG. 2B).The hexagonal lattice parameter of 5.0±0.2 A compares well with reportedvalues for SAMs of ODT on Au(111) (Id.) and shows that ODT, rather thansome other adsorbate (water or acetonitrile), was transported from thetip to the substrate.

Although the experiments performed on Au(111)/mica provided importantinformation about the chemical identity of the transported species inthese experiments, Au(111)/mica is a poor substrate for DPN. The deepvalleys around the small Au(111) facets make it difficult to draw long(micrometer) contiguous lines with nanometer widths.

The nonannealed Au substrates are relatively rough (root-mean squareroughness 2 nm), but 30 nm lines could be deposited by DPN (FIG. 2C).This distance is the average Au grain diameter of the thin filmsubstrates and represents the resolution limit of DPN on this type ofsubstrate. The 30-nm molecule-based line prepared on this type ofsubstrate was discontinuous and followed the grain edges of the Au.Smoother and more contiguous lines could be drawn by increasing the linewidth to 100 nm (FIG. 2D) or presumably by using a smoother Ausubstrate. The width of the line depends upon tip scan speed and rate oftransport of the alkanethiol from the tip to the substrate (relativehumidity can change the transport rate). Faster scan speeds and asmaller number of traces give narrower lines.

DPN was also used to prepare molecular dot features to demonstrate thediffusion properties of the “ink” (FIGS. 3A and 3B). The ODT-coated tipwas brought into contact (set point=1 nN) with the Au substrate for aset period of time. For example, 0.66 μm, 0.88 μm, and 1.6 μm diameterODT dots were generated by holding the tip in contact with the surfacefor 2, 4, and 1 6 minutes, respectively (left to right, FIG. 3A). Theuniform appearance of the dots likely reflects an even flow of ODT inall directions from the tip to the surface. Opposite contrast imageswere obtained by depositing dots of an alkanethiol derivative,16-mercaptohexadecanoic acid in an analogous fashion (FIG. 3B). This notonly provides additional evidence that the molecules are beingtransported from the tip to the surface but also demonstrates themolecular generality of DPN.

Arrays and grids could be generated in addition to individual lines anddots. An array of twenty-five 0.46-μm diameter ODT dots spaced 0.54 μmapart (FIG. 3C) was generated by holding an ODT-coated tip in contactwith the surface (1 nM) for 20 seconds at 45% relative humidity withoutlateral movement to form each dot. A grid consisting of eightintersecting lines 2 μm in length and 100 nm wide (FIG. 3D) wasgenerated by sweeping the ODT-coated tip on a Au surface at a 4 μm persecond scan speed with a 1 nN force for 1.5 minutes to form each line.

Example 2 “Dip Pen” Nanolithography with a Variety of Substrates and“Inks”

A large number of compounds and substrates have been successfullyutilized in DPN. They are listed below in Table 1, along with possibleuses for the combinations of compounds and substrates.

AFM tips (Park Scientific) were used. The tips were silicon tips,silicon nitride tips, and silicon nitride tips coated with a 10 nm layerof titanium to enhance physisorption of patterning compounds. Thesilicon nitride tips were coated with the titanium by vacuum depositionas described in Holland, Vacuum Deposition Of Thin Films (Wiley, NewYork, N.Y., 1956). It should be noted that coating the silicon nitridetips with titanium made the tips dull and decreased the resolution ofDPN. However, titanium-coated tips are useful when water is used as thesolvent for a patterning compound. DPN performed with uncoated siliconnitride tips gave the best resolution (as low as about 10 nm).

Metal film substrates listed in Table 1 were prepared by vacuumdeposition as described in Holland, Vacuum Deposition Of Thin Films(Wiley, New York, N.Y., 1956). Semiconductor substrates were obtainedfrom Electronic Materials, Inc., Silicon Quest, Inc. MEMS TechnologyApplications Center, Inc., or Crystal Specialties, Inc.

The patterning compounds listed in Table 1 were obtained from AldrichChemical Co. The solvents listed in Table 1 were obtained from FisherScientific.

The AFM tips were coated with the patterning compounds as described inExample 1 (dipping in a solution of the patterning compound followed bydrying with an inert gas), by vapor deposition or by direct contactscanning. The method of Example 1 gave the best results. Also, dippingand drying the tips multiple times further improved results.

The tips were coated by vapor deposition as described in Sherman,Chemical Vapor Deposition For Microelectronics: Principles, TechnologyAnd Applications (Noyes, Park Ridges, N.J., 1987). Briefly, a patterningcompound in pure form (solid or liquid, no solvent) was placed on asolid substrate (e.g., glass or silicon nitride; obtained from FisherScientific or MEMS Technology Application Center) in a closed chamber.For compounds which are oxidized by air, a vacuum chamber or anitrogen-filled chamber was used. The AFM tip was position about 1-20 cmfrom the patterning compound, the distance depending on the amount ofmaterial and the chamber design. The compound was then heated to atemperature at which it vaporizes, thereby coating the tip with thecompound. For instance, 1-octadecanethiol can be vapor deposited at 60°C. Coating the tips by vapor deposition produced thin, uniform layers ofpatterning compounds on the tips and gave quite reliable results forDPN.

The tips were coated by direct contact scanning by depositing a drop ofa saturated solution of the patterning compound on a solid substrate(e.g., glass or silicon nitride; obtained from Fisher Scientific or MEMSTechnology Application Center). Upon drying, the patterning compoundformed a microcrystalline phase on the substrate. To load the patterningcompound on the AFM tip, the tip was scanned repeatedly (−5 Hz scanspeed) across this microcrystalline phase. While this method was simple,it did not lead to the best loading of the tip, since it was difficultto control the amount of patterning compound transferred from thesubstrate to the tip.

DPN was performed as described in Example 1 using a Park Scientific AFM,Model CP, scanning speed 5-10 Hz. Scanning times ranged from 10 secondsto 5 minutes. Patterns prepared included grids, dots, letters, andrectangles. The width of the grid lines and the lines that formed theletters ranged from 15 nm to 250 nm, and the diameters of the individualdots ranged from 12 nm to 5 micrometers. TABLE 1 Patterning CommentsSub- Compound/ Potential and strate Solvent(s) Applications ReferencesAu n-octadecanethiol/ Basic research Study of inter- acetonitrile,molecular forces, Langmuir 10, ethanol 3315 (1994) Etching resist forEtchant: KCN/O₂ microfabrication (pH ˜ 14), J. Vac. Sci. Tech. B, 13,1139 Dodecanethiol/ Molecular Insulating thin acetonitrile, electronicscoating on nano- ethanol meter scale gold clusters. Super- lattices andMicro- structures 18, 275 (1995) n-hexadecanethiol/ Etching resist forEtchant: KCN/O₂ acetonitrile, microfabrication (pH ˜ 14). ethanolLangmuir, 15, 300 (1999) n-docosanethiol/ Etching resist for Etchant:KCN/O₂ acetonitrile, microfabrication (pH ˜ 14). J. ethanol Vac. Sci.Technol. B, 13, 2846 (1995) 11-mercapto-1- Surface Capturing SiO₂undecanol/ functionalization clusters acetonitrile, ethanol16-mercapto-1- Basic research Study of Inter- hexadecanoic acid/molecular forces. acetonitrile, Langmuir 14, 1508 ethanol. (1998)Surface Capturing SiO₂, functionalization SnO₂ clusters. J. Am. Chem.Soc., 114, 5221 (1992) Octanedithiol/ Basic research Study of inter-acetonitrile, molecular forces. ethanol Jpn. J. Appl. Phys. 37, L299(1998) Hexanedithiol/ Surface Capturing gold acetonitrite,functionalization clusters. J. Am. ethanol Chem. Soc., 114, 5221 (1992)Propariedithiol/ Basic research Study of inter- acetonitrile, molecularforces. ethanol J. Am. Chem. Soc., 114, 5221 (1992) α,α′-p-xylyldithiol/Surface Capturing gold acetonitrile, functionalization clusters.Science, ethanol 272, 1323 (1996) Molecular Conducting nano- electronicsmeter scale Science, 272, 1323 (1996) 4,4′-biphenyldithiol/ SurfaceCapturing gold and acetonitrile, functionalization CdS clusters, ethanolInorganica Chemica Acta 242, 115 (1996) Terphenyldithiol/ SurfaceCapturing gold and acetonitrile, functionalization CdS clusters, ethanolInorganica Chemica Acta 242, 115 (1996) terphenyldiisocyanide/ SurfaceCapturing gold and acetonitrile, functionalization CdS clusters,methylene Inorganica Chemica chloride Acta 242, 115 (1996) MolecularConductive coating electronics on nanometer scale gold clusters.Superlattices and Microstructures, 18, 275 (1995) DNA/water: Gene DNAprobe to acetonitrile (1.3) detection detect biological cells. J. Am.Chem. Soc. 119, 8916 (1997) Ag n-hexadecanethiol/ Etching resist forEtchant: Fe(NO₃)₃ acetonitrile, microfabrication (pH ˜ 6). Micro-ethanol lectron. Eng., 32, 255 (1996) Al 2-mercaptoacetic acid/ SurfaceCapturing CdS acetonitrile, functionalization clusters. J. Am. ethanolChem. Soc., 114, 5221 (1992) GaAs- n-octadecanethiol/ Basic researchSelf assembled 100 acetonitrile monolayer ethanol formation Etchingresist for HCl/HNO₃(pH ˜ 1). microfabrication J. Vac. Sci. Technol. B,11, 2823 (1993) TiO2 n-octadecanethiol/ Etching resist for acetonitrile,microfabrication ethanol SiO2 16-mercapto-1- Surface Capturing gold andhexadecanoic acid/ functionalization CdS clusters acetonitrile, ethanoloctadecyltrichlorosila Etching resist for Etchant: HF/NH₄F ne(OTS,microfabrication (pH ˜ 2). Appl. CH₃(ch₂)₁₇SiCl₃) Phys. Lett., 70, 1.2nm thick SAM/ 1593 (1997) hexane APTS, 3-(2- Surface Capturing nano-Aminoethylamino)pro functionalization meter scale goldpoltrimethoxysilane/ clusters Appl. Phys. water Lett. 70, 2759 (1997)

Example 3 Atomic Force Microscopy with Coated Tips

As noted above, when an AFM is operated in air, water condenses betweenthe tip and surface and then is transported by means of the capillary asthe tip is scanned across the surface. Piner et al., Langmuir 13,6864-6868 (1997). Notably, this filled capillary, and the capillaryforce associated with it, significantly impede the operation of the AFM,especially when run in lateral force mode. Noy et al., J. Am. Chem. Soc.117, 7943-7951 (1995); Wilbur et al., Langmuir 11, 825-831 (1995). Inair, the capillary force can be 10 times larger than chemical adhesionforce between tip and sample. Therefore, the capillary force cansubstantially affect the structure of the sample and the imagingprocess. To make matters worse, the magnitude of this effect will dependon many variables, including the relative hydrophobicities of the tipand sample, the relative humidity, and the scan speed. For thesereasons, many groups have chosen to work in solution cells where theeffect can be made more uniform and reproducible. Frisbie et al.,Science 265, 2071-2074 (1994); Noy et al., Langmuir 14, 1508-1511(1998).This, however, imposes a large constraint on the use of an AFM, andsolvent can affect the structure of the material being imaged. Vezenovet al., J. Am. Chem. Soc. 119, 2006-2015 (1997). Therefore, othermethods that allow one to image in air with the capillary effect reducedor eliminated would be desirable.

This example describes one such method. The method involves themodification of silicon nitride AFM tips with a physisorbed layer of1-dodecylamine. Such tips improve one's ability to do LFM in air bysubstantially decreasing the capillary force and providing higherresolution, especially with soft materials.

All data presented in this example were obtained with a Park ScientificModel CP AFM with a combined AFM/LFM head. Cantilevers (model no.MLCT-AUNM) were obtained from Park Scientific and had the followingspecifications: gold coated microlever, silicon nitride tip, cantileverA, spring constant=0.05 N/m. The AFM was mounted in a Park vibrationisolation chamber which had been modified with a dry nitrogen purgeline. Also, an electronic hygrometer, placed inside the chamber, wasused for humidity measurements (±5% with a range of 12˜100%). Muscovitegreen mica was obtained from Ted Pella, Inc. Soda lime glass microscopeslides were obtained from Fisher. Polystyrene spheres with 0.23±0.002 μmdiameters were purchased from Polysciences, and Si₃N₄ on silicon wasobtained from MCNC MEMS Technology Applications Center. 1-Dodecylamine(99+%) was purchased from Aldrich Chemical Inc. and used without furtherpurification. Acetonitrile (A.C.S. grade) was purchased from FisherScientific Instruments, Inc.

Two methods for coating an AFM tip with 1-dodecylamine were explored.The first method involved saturating ethanol or acetonitiile with1-dodecylamine and then depositing a droplet of this solution on a glasssubstrate. Upon drying, the 1-dodecylamine formed a microcrystallinephase on the glass substrate. To load the 1-dodecylamine on the AFM tip,the tip was scanned repeatedly (˜5 Hz scan speed) across thismicrocrystalline phase. While this method was simple, it did not lead tothe best loading of the tip, since it was difficult to control theamount of 1-dodecylamine transferred from the substrate to the tip.

A better method was to transfer the dodecylamine directly from solutionto the AFM cantilever. This method involved soaking the AFM cantileverand tip in acetonitrile for several minutes in order to remove anyresidual contaminants on the tip. Then the tip was soaked in a ˜5 mM1-dodecylamine/acetonitrile solution for approximately 30 seconds. Next,the tip was blown dry with compressed freon. Repeating this procedureseveral times typically gave the best results. The 1-dodecylamine isphysisorbed, rather than chemisorbed, onto the silicon nitride tips.Indeed, the dodecylamine can be rinsed off the tip with acetonitrile asis the case with bulk silicon nitride. Benoit et al. Microbeam andNanobeam Analysis; Springer Verlag, (1996). Modification of the tip inthis manner significantly reduced the capillary effects due toatmospheric water condensation as evidenced by several experimentsdescribed below.

First, a digital oscilloscope, directly connected to the lateral forcedetector of the AFM, was used to record the lateral force output as afunction of time. In this experiment, the force of friction changeddirection when the tip scanned left to right, as compared with right toleft. Therefore, the output of the LFM detector switched polarity eachtime the tip scan direction changed. If one or more AFM raster scanswere recorded, the output of the detector was in the form of a squarewave, FIG. 4AB. The height of the square wave is directly proportionalto the sliding friction of the tip on the sample and, therefore, one cancompare the forces of friction between an unmodified tip and a glasssubstrate and between a modified tip and a glass substrate simply bycomparing the height of the square waves under nearly identical scanningand environmental conditions. The tip/sample frictional force was atleast a factor of three less for the modified tip than for theunmodified tip. This experiment was repeated on a mica substrate, and asimilar reduction in friction was observed. In general, reductions infriction measured in this way and under these conditions ranged from afactor of three to more than a factor of ten less for the modified tips,depending upon substrate and environmental conditions, such as relativehumidity.

While this experiment showed that 1-dodecylamine treatment of an AFM tiplowered friction, it did not prove that water and the capillary forcewere the key factors. In another experiment, the effects of the1-dodecylamine coating on the capillary transport of water was examined.Details of water transport involving unmodified tips have been discussedelsewhere. Finer et al., Langmuir 13, 6864-6868 (1997). When an AFM tipwas scanned across a sample, it transported water to the sample bycapillary action, FIG. 5A. After scanning a 4 μm×5 μm area of a sodaglass substrate for several minutes, contiguous adlayers of water weredeposited onto the substrate and imaged by LFM by increasing the scansize. Areas of lower friction, where water had been deposited, appeareddarker than non-painted areas, FIG. 5A. The same experiment conductedwith a tip coated with 1-dodecylamine did not show evidence ofsubstantial water transport, FIG. 5B. Indeed, only random variations infriction were observed.

While these experiments showed that friction could be reduced and thetransport of water from the tip to the substrate by capillary actioncould be inhibited by coating the tip with 1-dodecylamine, they did notprovide information about the resolving power of the modified tip. Micais an excellent substrate to evaluate this issue and, indeed, latticeresolved images could be routinely obtained with the modified tips,demonstrating that this modification procedure reduced the force offriction without blunting the tip, FIG. 6A. It was impossible todetermine whether the portion of the tip that was involved in theimaging was bare or had a layer of 1-dodecylamine on it. In fact, it islikely that the 1-dodecylamine layer had been mechanically removed fromthis part of the tip exposing the bare Si₃N₄. In any event, theremainder of the tip must have had a hydrophobic layer of dodecylamineon it, since water was inhibited from filling the capillary surroundingthe point of contact, thereby reducing the capillary effect (see above).

While the atomic scale imaging ability of the AFM was not adverselyaffected by the 1-dodecyl amine coating on the tip, the above experimentdid not provide useful information about the suitability of the tip forobtaining morphology data on a larger scale. In order to obtain suchinformation, a sample of monodisperse 0.23 μm diameter latex spheres wasimaged with both modified and unmodified tips. Since the topographyrecorded by an AFM is a convolution of the shape of the tip and theshape of the sample, any change in the shape of the tip will bereflected in a change in the imaged topography of the latex spheres. Nodetectable difference was found in images taken with unmodified andmodified tips, respectively, FIGS. 7A-B. This shows that the shape ofthe tip was not significantly changed as it would be if a metalliccoating had been evaporated onto it. Moreover, it suggests that the1-dodecylamine coating was fairly uniform over the surface of the tipand was sharp enough that it did not adversely affect atomic scaleimaging.

A significant issue pertains to the performance of the modified tips inthe imaging of soft materials. Typically, it is difficult to determinewhether or not a chemically-modified tip exhibits improved performanceas compared with a bare tip. This is because chemical modification isoften an irreversible process which sometimes requires the deposition ofan intermediary layer. However, since the modification process reportedherein was based upon physisorbed layers of 1-dodecylamine, it waspossible to compare the performance of a tip before modification, aftermodification, and after the tip had been rinsed and the 1-dodecylaminehad been removed. Qualitatively, the 1-dodecylamine-modified tips alwaysprovided significant improvements in the imaging of monolayers basedupon alkanethiols and organic crystals deposited onto a variety ofsubstrates. For example, a lattice resolved image of a hydrophilicself-assembled monolayer of 11-mercapto-1-undecanol on a Au(111) surfacewas routinely obtained with a modified tip, FIG. 6B. The lattice couldnot be resolved with the same unmodified AFM tip. On this surface, thecoated tip showed a reduction in friction of at least a factor of fiveby the square wave analysis (see above). It should be noted, that theOH-terminated SAM is hydrophilic and, hence, has a strong capillaryattraction to a clean tip. Reducing the capillary force by the modifiedtip allows one to image the lattice.

A second example of improved resolution involved imaging free standingliquid surfaces, such as water condensed on mica. It is well known thatat humidities between 30 and 40 percent, water has two distinct phaseson mica. Hu et al., Science 268, 267-269 (1995). In previous work bythis group, a non-contact mode scanning polarization force microscope(SPFM) was used to image these phases. It was found that, when a probetip came into contact with mica, strong capillary forces caused water towet the tip and strongly disturbed the water condensate on the mica. Toreduce the capillary effect so that two phases of water could be imaged,the tip was kept ˜20 nm away from the surface. Because of thisconstraint, one cannot image such phases with a contact mode scanningprobe technique. FIGS. 6C-D show images of the two phases of water onmica recorded at 30 percent humidity with a 1-dodecylamine modified tipin contact mode. The heights of the features (FIG. 6C) corresponded withthe frictional map (FIG. 6D), with higher features having lowerfriction. The quality of the modified tip, which it is believedcorrelates with the uniformity of the 1-dodecylamine layer on the tip,was important. Only well modified tips made it possible to image the twophases of water, while less well modified ones resulted in poorerquality images. In fact, this was such a sensitive test that it could beused as a diagnostic indicator of the quality of the1-dodecylamine-modified tips before proceeding to other samples.

In conclusion, this example describes a very simple, but extremelyuseful, method for making Si₃N₄ AFM tips hydrophobic. This modificationprocedure lowers the capillary force and improves the performance of theAFM in air. Significantly, it does not adversely affect the shape of theAFM tip and allows one to obtain lattice resolved images of hydrophilicsubstrates, including soft materials such as SAMs and even free-standingwater, on a solid support. The development of methodology that allowsone to get such information in air is extremely important because,although solution cells can reduce the effect of the capillary force,the structures of soft materials can be significantly affected bysolvent. Vezenov et al., J. Am. Soc. 119, 2006-2015 (1997). Finally,although it might be possible to make an AFM tip more hydrophobic byfirst coating it with a metal layer and then derivatizing the metallayer with a hydrophobic chemisorbed organic monolayer, it is difficultto do so without concomitantly blunting the AFM tip.

Example 4 Multicomponent “Dip Pen” Nanolithography

The inability to align nanoscale lithographically generated patternscomprised of chemically distinct materials is an issue that limits theadvancement of both solid-state and molecule-based nanoelectronics. Reedet al., Science 278, 252 (1997); Feldheim, et al., Chem. Soc. Rev. 27, 1(1998). The primary reasons for this problem are that many lithographicprocesses: 1) rely on masking or stamping procedures, 2) utilize resistlayers, 3) are subject to significant thermal drift problems, and 4)rely on optical-based pattern alignment. Campbell, The Science andEngineering of Microelectronic Fabrication (Oxford Press); Chou et al.,Appl. Phys. Lett. 67, 3114(1995); Wang et al., Appl. Phys. Lett. 70,1593 (1997); Jackman et al., Science 269, 664(1995); Kim et al., Nature376, 581(1995); Schoer et al., Langmuir 13,2323 (1997); Whelan et al.,Appl. Lett. 69, 4245 (1996); Younkin et al., Appl. Phys. Lett. 71, 1261(1997); Bottomley, Anal. Chem. 70, 425R. (1998); Nyffenegger and Penner,Chem. Rev. 97, 1195 (1997); Berggren, et al., Science 269, 1255 (1995);Sondag-Huethorst et al., Appl. Phys. Lett. 64, 285 (1994); Schoer andCrooks, Langmuir 13, 2323 (1997); Xu and Liu, Langmuir 13, 127 (1997);Perkins, et al., Appl. Phys. Lett. 68, 550 (1996); Carr, et al., J. Vac.Sci. Technol. A 15, 1446 (1997); Sugimura et al., J. Vac. Sci. Technol.A 14, 1223 (1996); Komeda et al., J. Vac. Sci. Technol. A 16, 1680(1998); Muller et al., J. Vac. Sci. Technol. B 13, 2846 (1995); and Kimand M. Lieber, Science 257, 375 (1992).

With respect to feature size, resist-based optical methods allow one toreproducibly pattern many materials, soft or solid-state, in the >100 nmline width and spatial resolution regime, while e-beam lithographymethods allow one to pattern in the 10-200 nm scale. In the case ofsoft-lithography, both e-beam lithography and optical methods rely onresist layers and the backfilling of etched areas with componentmolecules. This indirect patterning approach compromises the chemicalpurity of the structures generated and poses limitations on the types ofmaterials that can be patterned. Moreover, when more than one materialis being lithographically patterned, the optical-based pattern alignmentmethods used in these techniques limit their spatial resolution toapproximately 100 nm.

This example describes the generation of multicomponent nanostructuresby DPN, and shows that patterns of two different soft materials can begenerated by this technique with near-perfect alignment and 10 nmspatial resolution in an arbitrary manner. These results should openmany avenues to those interested in molecule-based electronics togenerate, align, and interface soft structures with each other andconventional macroscopically addressable microelectronic circuitry.

Unless otherwise specified, DPN was performed on atomically flat Au(111)substrates using a conventional instrument (Park Scientific CP AFM) andcantilevers (Park Scientific Microlever A). The atomically flat Au(111)substrates were prepared by first heating a piece of mica at 120° C. invacuum for 12 hours to remove possible water and then thermallyevaporating 30 nm of gold onto the mica surface at 220° C. in vacuum.Using atomically flat Au(111) substrates, lines 15 nm in width can bedeposited. To prevent piezo tube drift problems, a 100 μm scanner withclosed loop scan control (Park Scientific) was used for all experiments.The patterning compound was coated on the tips as described in Example 1(dipping in a solution) or by vapor deposition (for liquids andlow-melting-point solids). Vapor deposition was performed by suspendingthe silicon nitride cantilever in a 100 ml reaction vessel 1 cm abovethe patterning compound (ODT). The system was closed, heated at 60° C.for 20 min, and then allowed to cool to room temperature prior to use ofthe coated tips. SEM analysis of tips before and after coating bydipping in a solution or by vapor deposition showed that the patterningcompound uniformly coated the tips. The uniform coating on the tipsallows one to deposit the patterning compound on a substrate in acontrolled fashion, as well as to obtain high quality images.

Since DPN allows one to image nanostructures with the same tool used toform them, there was the tantalizing prospect of generatingnanostructures made of different soft materials with excellent registry.The basic idea for generating multiple patterns in registry by DPN isrelated to analogous strategies for generating multicomponent structuresby e-beam lithography that rely on alignment marks. However, the DPNmethod has two distinct advantages, in that it does not make use ofresists or optical methods for locating alignment marks. For example,using DPN, one can generate 15 nm diameter self-assembled monolayer(SAM) dots of 1,16-mercaptohexadecanoic acid (MHA) on a Au(111) facetedsubstrate (preparation same as described above for atomically flatAu(111) substrates) by holding an MHA-coated tip in contact (0.1 nN)with the Au(111) surface for ten seconds (see FIG. 9A). By increasingthe scan size, the patterned dots are then imaged with the same tip bylateral force microscopy (LFM). Since the SAM and bare gold have verydifferent wetting properties, LFM provides excellent contrast. Wilbur etal., Langmuir 11,825 (1995). Based upon the position of the firstpattern, the coordinates of additional patterns can be determined (seeFIG. 9B), allowing for precise placement of a second pattern of MHAdots. Note the uniformity of the dots (FIG. 9A) and that the maximummisalignment of the first pattern with respect to the second pattern isless than 10 nm (see upper right edge of FIG. 9C). The elapsed timebetween generating the data in FIGS. 9A and 9C was 10 minutes,demonstrating that DPN, with proper control over environment, can beused to pattern organic monolayers with a spatial and pattern alignmentresolution better than 10 nm under ambient conditions.

This method for patterning with multiple patterning compounds requiredan additional modification of the experiment described above. Since theMHA SAM dot patterns were imaged with an tip coated with a patterningcompound, it is likely that a small amount of undetectable patterningcompound was deposited while imaging. This could significantly affectsome applications of DPN, especially those dealing with electronicmeasurements on molecule-based structures. To overcome this problem,micron-scale alignment marks drawn with an MHA-coated tip (cross-hairson FIG. 10A) were used to precisely place nanostructures in a pristinearea on the Au substrate. In a typical experiment, an initial pattern of50 nm parallel lines comprised of MHA and separated by 190 nm wasprepared (see FIG. 10A). This pattern was 2 μm away from the exterioralignment marks. Note that an image of these lines was not taken toavoid contamination of the patterned area. The MHA-coated tip was thenreplaced with an ODT-coated tip. This tip was used to locate thealignment marks, and then precalculated coordinates based upon theposition of the alignment marks (FIG. 10B) were used to pattern thesubstrate with a second set of 50 nm parallel ODT SAM lines (see FIG.10C). Note that these lines were placed in interdigitated fashion andwith near-perfect registry with respect to the first set of MHA SAMlines (see FIG. 10C).

There is one unique capability of DPN referred to as “overwriting.”Overwriting involves generating one soft structure out of one type ofpatterning compound and then filling in with a second type of patterningcompound by raster scanning across the original nanostructure. As afurther proof-of concept experiment aimed at demonstrating themultiple-patterning-compound, high-registry, and overwritingcapabilities of DPN over moderately large areas, a MHA-coated tip wasused to generate three geometric structures (a triangle, a square, and apentagon) with 100 nm line widths. The tip was then changed to anODT-coated tip, and a 10 μm by 8.5 μm area that comprised the originalnanostructures was overwritten with the ODT-coated tip by rasterscanning 20 times across the substrate (contact force ˜0.1 nN) (darkareas of FIG. 11). Since water was used as the transport medium in theseexperiments, and the water solubilities of the patterning compounds usedin these experiments are very low, there was essentially no detectableexchange between the molecules used to generate the nanostructure andthe ones used to overwrite on the exposed gold (see FIG. 11).

In summary, the high-resolution, multiple-patterning-compoundregistration capabilities of DPN have been demonstrated. On anatomically flat Au(111) surface, 15 nm patterns were generated with aspatial resolution better than 10 nm. Even on a rough surface such asamorphous gold, the spatial resolution was better than conventionalphotolithographic and e-beam lithographic methods for patterning softmaterials.

Example 5 Use of DPN to Generate Resists

Lithographic techniques such as photolithography (Wallraff and Hinsberg,Chem. Rev., 99:1801(1999)), electron beam lithography (Wallraff andHinsberg, Chem. Rev., 99:1801 (1999); Xia et al., Chem. Rev., 99:1823(1999)), and microcontact printing (Xia et al., Chem. Rev., 99:1823(1999)) can be used with varying degrees of ease, resolution, and costto generate three-dimensional features on silicon wafers. DPN iscomplementary to these other nanolithographic techniques and can be usedwith conventional laboratory instrumentation (an AFM) in routine fashionto generate patterns of, e.g., alkylthiols on polycrystalline goldsubstrates, under ambient conditions. Moreover, DPN offers 15 nmlinewidth and 5 nm spatial resolution with conventional AFM cantilevers(see prior examples; Piner et al., Science, 283:661 (1999); Piner etal., Langmuir, 15:5457 (1999); Hong et al., Langmuir, 15:7897 (1999);Hong et al., Science, 286:523 (1999)).

Three-dimensional architectures on and in silicon are vital to themicroelectronics industry and, increasingly, are being applied to otheruses in microfabrication (Xia and Whitesides, Angew, Chem. Int. Ed.Engl., 37:550 (1998)). For example, the anisotropic etching of siliconcommonly yields narrow grooves, cantilevers, and thin membranes (Seidelet al., J. Electrochem. Soc., 137:3612 (1990)), which have been used forsensors of pressure, actuators, micro-optical components, and masks forsubmicron lithography techniques (Seidel et al., J. Electrochem. Soc.,137:3612 (1990)). For both the microeletronics applications and othermicrofabricated devices, significant advantages are expected from beingable to make smaller feature sizes (Xia and Whitesides, Angew, Chem.Int. Ed Engl., 37:550 (1998)). Additionally, the ability to fabricatesmaller scale structures can lead to the discovery or realization ofphysical and chemical properties fundamentally different from thosetypically associated with larger structures. Examples include Coulombblockades, single-electron tunneling, quantum size effects, catalyticresponse, and surface plasmon effects (Xia and Whitesides, Angew, Chem.Int. Ed Engl., 37:550 (1998)). Therefore, a range of applications isenvisioned for the custom-generated solid-state features potentiallyattainable through DPN and wet chemical etching.

Consequently, the suitability of DPN-generated nanostructures as resistsfor generating three-dimensional multilayered solid-state structures bystandard wet etching techniques was evaluated in a systematic study, theresults of which are reported in this example. In this study, DPN wasused to deposit alkylthiol monolayer resists on Au/Ti/Si substrates.Subsequent wet chemical etching yielded the targeted three-dimensionalstructures. Many spatially separated patterns of the monolayer resistscan be deposited by DPN on a single AU/Ti/Si chip and, thus, the effectsof etching conditions can be examined on multiple features incombinatorial fashion.

As diagrammed in FIG. 12, in a typical experiment in this study, DPN wasused to deposit alkylthiols onto an Au/Ti/Si substrate. It has been wellestablished that alkyithiols form well-ordered mono layers on Au thinfilms that protect the underlying Au from dissolution during certain wetchemical etching procedures (Xia et al., Chem. Mater., 7:23 32 (1995);Kumar et al., J. Am. Chem. Soc., 114:9188 (1992)), and this appears toalso hold true for DPN-generated resists (see below). Thus, the Au, Ti,and SiO₂ which were not protected by the monolayer could be removed bychemical etchants in a staged procedure (FIG. 12, panels b-e). Thisprocedure yielded “first-stage” three-dimensional features: multilayer,Au-topped features on the Si substrate (FIG. 12, panel b). Furthermore,“second-stage” features were prepared by using the remaining Au as anetching resist to allow for selective etching of the exposed Sisubstrate (FIG. 12, panels c and d). Finally, the residual Au wasremoved to yield final-stage all-Si features, FIG. 12, panel e. Thus,DPN can be combined with wet chemical etching to yield three-dimensionalfeatures on Si(100) wafers with at least one dimension on the sub-100 nmlength scale.

Specifically, FIG. 12 diagrams the procedure used to prepare nanoscalefeatures on Si wafers. First, polished single-crystalline Si(100) waferswere coated with 5 nm of Ti, followed by 10 nm of Au by thermalevaporation. The Si(100) wafers (4″ diameter (1-0-0) wafers; 3-4.9ohm/cm resistivity; 500-550 μm thickness) were purchased from SiliconQuest International, Inc. (Santa Clara, Calif.). Thermal evaporation of5 nm of Ti (99.99%; Alfa Aesar; Ward Hill, Mass.) followed by 10 nm ofAu (99.99%; D.F. Goldsmith; Evanston, Ill.) was accomplished using anEdwards Auto 306 Turbo Evaporator equipped with a turbopump (ModelEXT510) and an Edwards FTM6 quartz crystal microbalance to determinefilm thickness. Au and Ti depositions were conducted at room temperatureat a rate of 1 nm/second and a base pressure of <9×10⁻⁷ mb.

After Au evaporation, the following procedure was performed on thesubstrates: a) DPN was used to deposit patterns of ODT, b) Au and Tiwere etched from the regions not protected by the ODT monolayers using apreviously reported ferri/ferrocyanide based etchant (Xia et al., Chem.Mater., 7:2332 (1995)), c) residual Ti and SiO₂ were removed byimmersing the sample into a 1% HF solution (note: this procedure alsopassivates the exposed Si surfaces with respect to native oxide growth)(Ohmi, J. Electrochem. Soc., 143:2957(1996)), and d) the remaining Siwas etched anisotropically by minor modifications of a previouslyreported basic etchant (Seidel et al., J. Electrochem. Soc., 137:3612(1990)). The topography of the resulting wafers was evaluated by AFM andSEM.

All DPN and all AFM imaging experiments were carried out with aThermomicroscopes CP AFM and conventional cantilevers (Thermomicroscopessharpened Microlever A, force constant 0.05 N/m, Si₃N₄). A contact forceof 0.5 nN was typically used for DPN patterning. To minimize piezo tubedrift problems, a 100-μm scanner with closed loop scan control was usedfor all of the experiments. For DPN, the tips were treated with ODT inthe following fashion: 1) tips were soaked in 30% H₂O, H,SO₄ (3:7)(caution: this mixture reacts violently with organic material) for 30minutes, 2) tips were rinsed with water, 3) tips were heated in anenclosed canister (approximately 15 cm³ internal volume) with 200 mg ODTat 60° C. for 30 minutes, and 4) tips were blown dry with compresseddifluoroethane prior to use. Typical ambient imaging conditions were 30%humidity and 23° C., unless reported otherwise. Scanning electronmicroscopy (SEM) was performed using a Hitachi SEM equipped with EDSdetector.

A standard ferri/ferrocyanide etchant was prepared as previouslyreported (Xia et al., Chem. Mater., 7:2332 (1995)) with minormodification: 0.1 MNa₁S,O₃, 1.0 M KOH, 0.01 M K₃Fe(CN)₅, 0.001 MK₄Fe(CN)₆ in nanopure water. Au etching was accomplished by immersingthe wafer in this solution for 2-5 minutes while stirring. The HFetchant (1% (v:v) solution in nanopure water) was prepared from 49% HFand substrates were agitated in this solution for 10 seconds. Siliconetching was accomplished by immersing the wafer in 4 M KOH in 15% (v:v)isopropanol in nanopure water at 55° C. for 10 seconds while stirring(Seidel et al., J. Electrochem. Soc., 137:3612 (1990)). Finalpassivation of the Si substrate with respect to SiO, growth was achievedby immersing the samples in 1% HF for 10 seconds with mild agitation.Substrates were rinsed with nanopure water after each etching procedure.To remove residual Au, the substrates were cleaned in O₂ plasma for 3minutes and soaked in aqua regia (3:1 HCl:HNO₃) for 1 minute, followedby immersing the samples in 1% HF for 10 seconds with mild agitation.

FIG. 13A shows the AFM topography images of an AU/Ti/Si chip patternedaccording to the procedure outlined in FIG. 12, panels a-d. This imageshows four pillars with a height of 55 nm formed by etching an AU/Ti/Sichip patterned with four equal-sized dots of ODT with center-to-centerdistances of 0.8 μm. Each ODT dot was deposited by holding the AFM tipin contact with the Au surface for 2 seconds. Although the sizes of theODT dots were not measured prior to etching, their estimated diameterswere approximately 100 nm. This estimate is based upon the measuredsizes of ODT “test” patterns deposited with the same tip on the samesurface immediately prior to deposition of the ODT dots corresponding tothe shown pillars. The average diameter of the shown pillar tops was 90nm with average base diameter of 240 nm. FIG. 13B shows a pillar(55 nmheight, 45 nm top diameter, and 155 nm base diameter) from a similarlypatterned and etched region on the same Au/Ti/Si substrate. Thecross-sectional topography trace across the pillar diameter showed aflat top and symmetric sidewalls, FIG. 13C. The shape of the structuremay be convoluted by the shape of the AFM tip (approximately 10 nmradius of curvature), resulting in side widths as measured by AFM whichmay be larger than the actual widths.

Additionally, an AU/Ti/Si substrate was patterned with three ODT linesdrawn by DPN (0.4 μm/second, estimated width of each ODT line is 100 nm)with 1 μm center-to-center distances. FIG. 14A shows the AFM topographyimage after etching this substrate according to FIG. 12, panels a-d. Thetop and base widths are 65 nm and 415 nm, respectively, and line heightsare 55 nm. FIG. 14B shows a line from a similarly patterned and etchedregion on the same Au/Ti/Si wafer, with a 50 nm top width, 155 nm basewidth, and 55 nm height. The cross-sectional topography trace across theline diameter shows a flat top and symmetric sidewalls (FIG. 14C).

FIGS. 15 and 16 show the feature-size variation possible with thistechnique. In FIG. 15A, the ODT-coated AFM tip was held in contact withthe surface for varying lengths of time (16-0.062 seconds) to generatevarious sized dots with 2 μm center-to-center distances whichsubsequently yielded etched three-dimensional structures with topdiameters ranging from 1.47 μm to 147 nm and heights of 80 nm. The topdiameters as measured by SEM differed by less than 15% from thediameters measured from the AFM images, compare FIGS. 15A and 15B.Additionally, energy dispersive spectroscopy (EDS) showed the presenceof Au on the pillar tops whereas Au was not observed in the areassurrounding the elevated micro- and nanostructures. As expected, thediameters of the micro- and nano-trilayer structures correlated with thesize of the DPN-generated resist features, which was directly related totip-substrate contact time, FIG. 15C. Line structures were alsofabricated in combinatorial fashion, FIG. 16. ODT lines were drawn at ascan rate varying from 0.2-2.8 μm/second with 1 μm center-to-centerdistances. After etching, these resists afforded trilayer structures,all with a height of 80 nm and top line widths ranging from 505 to 50nm, FIG. 16. The field emission scanning electron micrograph of thepatterned area looks comparable to the AFM image of the same area withthe top widths as determined by the two techniques being within 15% ofone another, compare FIGS. 16A and 16B.

In conclusion, it has been demonstrated that DPN can be used to depositmonolayer-based resists with micron to sub-100 nm dimensions on thesurfaces of Au/Ti/Si trilayer substrates. These resists can be used withwet chemical etchants to remove the unprotected substrate layers,resulting in three-dimensional solid-state feature with comparabledimensions. It is important to note that this example does not addressthe ultimate resolution of solid-state nano structure fabrication bymeans of DPN. Indeed, it is believed that the feature size will decreasethrough the use of new “inks” and sharper “pens.” Finally, this workdemonstrates the potential of using DPN to replace the complicated andmore expensive hard lithography techniques (e.g. e-beam lithography) fora variety of solid-state nanolithography applications.

Example 6 Multi-Pen Nanoplotter for Serial and Parallel DPN

The largest limitation in using scanning probe methodologies for doingultra-high-resolution nanolithography over large areas derives from theserial nature of most of these techniques. For this reason, scanningprobe lithography (SPL) methods have been primarily used ascustomization tools for preparing and studying academic curiosities(Snow et al., Appl. Phys. Lett., 75:1476 (1999); Luthi et al., Appl.Phys. Lett., 75:1314 (1999); Bottomley, Anal. Chem., 70:425R (1998);Schoer and Crooks, Langmuir, 13:2323 (1997); Xu and Liu, Langmuir,13:127 (1997); Nyffenegger and Penner, Chem. Rev., 97:1195 (1997);Sugimur and Nakagiri, J. Vac. Sci. Technol. A, 14:1223 (1996); Muller etal., J. Vac. Sci. Technol. B, 13:2846 (1995); Jaschke and Butt,Langmuir, 11:1061 (1995); Kim and Lieber, Science, 257:375 (1992)). IfSPL methodologies are ever to compete with optical or even stampinglithographic methods for patterning large areas (Xia et al., Chem. Rev.,99:1823 (1999); Jackman et al., Science, 269:664(1995); Chou et al.,Appl. Phys. Lett., 67:3114(1995)), they must be converted from serial toparallel processes. Several important steps have been taken in thisdirection. For example, researchers have developed a variety ofdifferent scanning multiple probe instruments (Lutwyche et al., Sens.Actuators A, 73:89 (1999); Vettiger et al, Microelectron Eng., 46:11(1999); Mime et al., Appl. Phys. Lett., 73:1742 (1998); Tsukamoto etal., Rev. Sd. Instrum., 62:1767 (1991)), and some have begun to usethese instruments for parallel SPL. In particular, Quate and coworkershave shown that as many as 50 tips could be used at once (Minne et al.,Appl. Phys. Lett., 73:1742 (1998)), and with such a strategy, bothimaging and patterning speeds could be dramatically improved. However, amajor limitation of all parallel SPL methods thus far developed is thateach tip within the array needs a separate feedback system, whichdramatically increases the instrumentation complexity and cost. One ofthe reasons separate feedback systems are required in such a process isthat tip-substrate contact force influences the line width and qualityof the patterned structure. Although parallel scanning tunnelingmicroscope (STM) lithography has not yet been demonstrated, such aprocess would presumably require a feedback system for each tip thatallows one to maintain constant tunneling currents. Like most other SPLmethods, DPN thus far has been used exclusively in a serial format.Herein, a method for doing parallel or single pen soft nanolithographyusing an array of cantilevers and a conventional AFM with a single feedback system is reported.

There is a key scientific observation that allows one to transform DPNfrom a serial to parallel process without substantially complicating theinstrumentation required to do DPN. It has been discovered that features(e.g. dots and lines) generated from inks such as 1-octadecanethiol(ODT), under different contact forces that span a two-order of magnituderange, are virtually identical with respect to diameter and line-width,respectively. Surprisingly, even patterning experiments conducted with asmall negative contact force, where the AFM tip bends down to thesurface, exhibit ink transport rates that are comparable to experimentsexecuted with the tip-substrate contact force as large as 4 nN (FIG.19). These experiments clearly showed that, in DPN writing, the inkmolecules migrate from the tip through the meniscus to the substrate bydiffusion, and the tip is simply directing molecular flow.

The development of an eight pen nanoplotter capable of doing parallelDPN is described in this example. Significantly, since DPN line widthand writing speed are independent of contact force, this has beenaccomplished in a configuration that uses a single tip feedback systemto monitor a tip with dual imaging and writing capabilities (designatedthe “imaging tip”). In parallel writing mode, all other tips reproducewhat occurs at the imaging tip in passive fashion. Experiments thatdemonstrate eight-pen parallel writing, ink and rinsing wells, and“molecular corralling” by means of a nanoplotter-generated structure arereported.

All experiments were performed on a Thermomicroscopes MS AFM equippedwith a closed loop scanner that minimizes thermal drift. Custom DPNsoftware (described above) was used to drive the instrument. Theinstrument has a 200 mm×200 mm sample holder and an automatedtranslation stage.

The intention in transforming DPN into a parallel process was to createan SPL method that allows one to generate multiple single-ink patternsin parallel or a single multiple-ink pattern in series. This tool wouldbe the nanotechnologist's equivalent of a multiple-pen nanoplotter withparallel writing capabilities. To accomplish this goal, severalmodifications of the AFM and DPN process were required (see FIGS. 17 and18).

First, a tilt stage (purchased from Newport Corporation) was mounted onthe translation stage of the AFM. The substrate to be patterned wasplaced in the sample holder, which was mounted on the tilt stage. Thisarrangement allows one to control the orientation of the substrate withrespect to the ink coated tips which, in turn, allows one to selectivelyengage single or multiple tips during a patterning experiment (FIG. 17).

Second, ink wells, which allow one to individually address and ink thepens in the nanoplotter, were fabricated. Specifically, it has beenfound that rectangular pieces of filter paper soaked with different inksor solvents can be used as ink wells and rinsing wells, respectively(FIG. 17). The filter-paper ink and rinsing wells were located on thetranslation stage proximate the substrate. An AFM tip can be coated witha molecular ink of interest or rinsed with a solvent simply by makingcontact with the appropriate filter-paper ink or rinsing well for 30seconds (contact force=1 nN).

Finally, a multiple tip array was fabricated simply by physicallyseparating an array of cantilevers from a commercially available waferblock containing 250 individual cantilevers (Thermomicroscopes SharpenedMicrolevers C, force constant=0.01 N/m), and then, using that array as asingle cantilever (FIG. 18). The array was affixed to a ceramic tipcarrier that comes with the commercially acquired mounted cantileversand was mounted onto the AFM tip holder with epoxy glue (FIG. 18).

For the sake of simplicity, experiments involving only two cantileversin the array will be described first. In parallel writing, one tip,designated “the imaging tip,” is used for both imaging and writing,while the second tip is used simply for writing. The imaging tip is usedthe way a normal AFM tip is used and is interfaced with force sensorsproviding feedback; the writing tips do not need feedback systems. In apatterning experiment, the imaging tip is used to determine overallsurface topology, locate alignment marks generated by DPN, andlithographically pattern molecules in an area with coordinates definedwith respect to the alignment marks (Example 4 and Hong et al., Science,286:523 (1999)). With this strategy, the writing tip(s) reproduce thestructure generated with the imaging tip at a distance determined by thespacing of the tips in the cantilever array (600 μm in the case of a twopen experiment).

In a typical parallel, multiple-pen experiment involving a cantileverarray, each tip was coated with an ink by dipping it into theappropriate ink well. This was accomplished by moving the translationstage to position the desired ink well below the tip to be coated andlowering the tip until it touched the filter paper. Contact wasmaintained for 30 seconds, contact force=1 nN. To begin parallelpatterning, the tilt stage was adjusted so that the writing tip was 0.4μm closer to the sample than the imaging tip. The tip-to-sampledistances in an array experiment can be monitored with the Z-steppermotor counter. The laser was placed on the imaging tip so that duringpatterning both tips were in contact with the surface (FIG. 17).

The first demonstration of parallel writing involved two tips coatedwith the same ink, ODT (FIG. 20A). In this experiment, twoone-molecule-thick nanostructures comprised of ODT were patterned onto agold surface by moving the imaging tip along the surface in the form ofa square (contact force ˜0.1 nN; relative humidity 30%; writingspeed=0.6 μm/sec). Note that the line-widths are nearly identical andthe nanostructure registration (orientation of the first square withrespect to the second) is near-perfect.

Parallel patterning can be accomplished with more than one ink. In thiscase the imaging tip was placed in a rinsing well to remove the ODT inkand then coated with 16-mercaptohexadecanoic acid (MBA) by immersing itin an MBA ink well. The parallel multiple-ink experiment was thencarried out in a manner analogous to the parallel single ink experimentunder virtually identical conditions. The two resulting nanostructurescan be differentiated based upon lateral force but, again, are perfectlyaligned due to the rigid, fixed nature of the two tips (FIG. 20B).Interestingly, the line-widths of the two patterns were identical. Thislikely is a coincidental result since feature size and line width in aDPN experiment often depend on the transport properties of the specificinks and ink loading.

A remarkable feature of this type of nanoplotter is that, in addition tooffering parallel writing capabilities, one can operate the system inserial fashion to generate customized nanostructures made of differentinks. To demonstrate this capability, a cantilever array that had a tipcoated with ODT and a tip coated with MHA was utilized. The laser wasfocused on the ODT coated tip, and the tilt stage was adjusted so thatonly this tip was in contact with the surface (FIG. 17). The ODT coatedtip was then used to generate the vertical sides of a cross on a Ausurface (contact force ˜0.1 nN; relative humidity ˜30%; writingspeed=1.3 μm/second) (FIG. 21A). The laser was then moved to the MBAcoated tip, and the tilt stage was readjusted so that only this tip wasin contact with surface. The MHA tip was then used to draw the 30 nmwide horizontal sides of the nanostructure (“nano” refers to line width)(FIG. 21A). Microscopic ODT alignment marks deposited on the peripheryof the area to be patterned were used to locate the initialnanostructure as described above (see also Example 4 and Hong et al.,Science, 286:523 (1999)).

This type of multiple ink nanostructure with a bare gold interior wouldbe impossible to prepare by stamping methodologies or conventionalnanolithography methods, but was prepared in five minutes with themultiple-pen nanoplotter. Moreover, this tool and these types ofstructures can now be used to begin evaluating important-issuesinvolving molecular diffusion on the nanometer length scale and acrossnanometer wide molecule-based barriers. As a proof-of-concept, thediffusion of MHA from a tip to the surface within this type of“molecule-based corral” was examined. As a first step, a cross shape wasgenerated with a single ink, ODT (contact force ˜0.1 nN; relativehumidity ˜30%; writing speed=0.5 μm/second). Then, an MHA coated tip washeld in contact with the surface for ten minutes at the center of thecross so that MHA molecules were transported onto the surface and coulddiffuse out from the point of contact. Importantly, even 80 nm wide ODTlines acted as a diffusion barrier, and MBA molecules were trappedinside the ODT cross pattern (FIG. 21B). When the horizontal sides ofthe molecular corral are comprised of MHA barriers, the MHA moleculesdiffuse from tip onto the surface and over the hydrophilic MHA barriers.Interestingly, in this two component nanostructure, the MBA does not goover the MHA barriers, resulting in an anisotropic pattern (FIG. 21C).Although it is not known yet if the corral is changing the shape of themeniscus, which in turn controls ink diffusion, or alternatively, theink is deposited and then migrates from the point of contact to generatethis structure, this type of proof-of-concept experiment shows how onecan begin to discover and study important interfacial processes usingthis new nanotechnology tool.

The parallel nanoplotting strategy reported herein is not limited to twotips. Indeed, it has been shown that a cantilever array consisting ofeight tips can be used to generate nanostructures in parallel fashion.In this case, each of the eight tips was coated with ODT. The outermosttip was designated as the imaging tip and the feedback laser was focusedon it during the writing experiment. To demonstrate this concept, fourseparate nanostructures, a 180 nm dot (contact force ˜0.1 nN, relativehumidity=26%, contact time=1 second), a 40 nm wide line, a square and anoctagon (contact force 0.1 nN, relative humidity=26%, writing speed=0.5μm/second) were generated and reproduced in parallel fashion with theseven passively following tips (FIG. 22). Note that there is a less than10% standard deviation in line width for the original nanostructures andthe seven copies.

In summary, DPN has been transformed from a serial to a parallel processand, through such work, the concept of a multiple-pen nanoplotter withboth serial and parallel writing capabilities has been demonstrated. Itis important to note that the number of pens that can be used in aparallel DPN experiment to passively reproduce nanostructures is notlimited to eight. Indeed, there is no reason why the number of penscannot be increased to hundreds or even a thousand pens without the needfor additional feedback systems. Finally, this work will allowresearchers in the biological, chemical, physics, and engineeringcommunities to begin using DPN and conventional AFM instrumentation todo automated, large scale, moderately fast, high-resolution andalignment patterning of nanostructures for both fundamental science andtechnological applications.

Example 7 Use of DPN to Prepare Combinatorial Arrays

A general method for organizing micro- and nanoparticles on a substratecould facilitate the, formation and study of photonic band gapmaterials, make it possible to generate particle arrays for analysis ofthe relationship between pattern structure and catalytic activity, andenable formation of single protein particle arrays for proteomicsresearch. While several methods have been reported for assemblingcollections of particles onto patterned surfaces (van Blaaderen et al.,Nature 385:321-323 (1997); Sastry et al., Langmuir 16:3553-3 556 (2000);Tien et al., Langmuir 13:5349-5355 (1997); Chen et al., Langmuir16:7825-7834(2000); Vossmeyer et al., J Appl. Phys. 84:3664-3670(1998);Qin et al., Adv. Mater. 11:1433-1437 (1999)), a major challenge lies inthe selective immobilization of single particles into pre-determinedpositions with respect to adjacent particles.

A strategy for chemically and physically immobilizing a wide variety ofparticle types and sizes with a high degree of control over particleplacement calls for a soft lithography technique capable ofhigh-resolution patterning, but also with the ability to form patternsof one or more molecules with precision alignment registration. DPN issuch a tool. This example demonstrates combinatorial arrays produced byDPN, focusing on the problem of particle assembly in the context ofcolloidal crystallization.

Recently, conventional sedimentation methods for preparing colloidalcrystals consisting of close-packed layers of polymer or inorganicparticles (Park et al., Adv. Mater. 10:1028-1032 (1998), and referencescited therein; Jiang et al., Chem. Mater. 11:2132-2140 (1999)) have beencombined with polymer templates, fabricated by e-beam lithography, toform high quality single-component structures (van Blaaderen et al.,Nature 385:321-323 (1997)). However, sedimentation or solventevaporation routes do not offer the element of chemical control overparticle placement. Herein, a DPN-based strategy for generating chargedchemical templates to study the assembly of single particles intotwo-dimensional square lattices is described.

The general method (outlined in FIG. 23) is to form a pattern on asubstrate composed of an array of dots of an ink which will attract andbind a specific type of particle. For the present studies, MHA was usedto make templates on a gold substrate, and positively-charged protonatedamine- or amidine-modified polystyrene spheres were used as particlebuilding blocks.

Gold coated substrates were prepared as described in Example 5. For insitu imaging experiments requiring transparent substrates, glasscoverslips (Corning No. 1 thickness, VWR, Chicago, Ill.) were cleanedwith Ar/O—, plasma for 1 minute, then coated with 2 nm of Ti and 15 nmof Au. The unpatterned regions of the gold substrate were passivated byimmersing the substrate in a 1 mM ethanolic solution of anotheralkanethiol, such as ODT or cystamine. Minimal, if any, exchange tookplace between the immobilized MHA molecules and the ODT or cystamine insolution during this treatment, as evidenced by lateral force microscopyof the substrate before and after treatment with ODT.

The gold substrates were patterned with MHA to form arrays of dots. DPNpatterning was carried out under ambient laboratory conditions (30%humidity, 23° C.) as described in Example 5. It is important to notethat the carboxylic acid groups in the MHA patterns were deprotonatedproviding an electrostatic driving force for particle assembly. (Vezenovet al., J. Am. Chem. Soc. 119:2006-201 5 (1997))

Suspensions of charged polystyrene latex particles in water werepurchased from either Bangs Laboratories (0.93 μm, Fishers, Ind.) or IDCLatex (1.0 μm and 190 nm, Portland, Oreg.). Particles were rinsed freeof surfactant by centrifugation and redispersion twice in distilleddeionized water (18.1 MΩ) purified with a Barnstead (Dubuque, Iowa)NANOpure water system. Particle assembly on the substrate wasaccomplished by placing a 20 μl droplet of dispersed particles (10%wt/vol in deionized water) on the horizontal substrate in a humiditychamber (100% relative humidity). Gentle rinsing with deionized watercompleted the process.

Optical microscopy was performed using the Park Scientific CP AFM optics(Thermomicroscopes, Sunnyvale, Calif.) or, for in situ imaging, aninverted optical microscope (Axiovert 100A, Carl Zeiss, Jena, Germany)operated in differential interference contrast mode (DIC). Images werecaptured with a Penguin 600 CL digital camera (Pixera, Los Gatos,Calif.). Intermittent-contact imaging of particles was performed with aThermomicroscopes MS AFM using silicon ultralevers (Thermomicroscopes,spring constant=3.2 N/m). Lateral force imaging was carried out underambient laboratory conditions (30% humidity, 23° C.) and as previouslyreported (Weinberger et al., Adv. Mater. 12:1600-1603 (2000)).

In a typical experiment involving 0.93 μm diameter particles, multipletemplates were monitored simultaneously for particle assembly by opticalmicroscopy. In these experiments, the template dot diameter was variedto search for optimal conditions for particle-template recognition, FIG.24 (left to right). After 1 hour of particle assembly, the substrateswere rinsed with deionized water, dried under ambient laboratoryconditions, and then imaged by optical microscopy, FIG. 25. Thecombinatorial experiment revealed that the optimum size of the templatepad with which to immobilize a single particle of this type in highregistry with the pattern was approximately 500-750 nm. It is importantto note that drying of the substrate tended to displace the particlesfrom their preferred positions on the template, an effect that has beennoted by others with larger scale experiments (Aizenberg et al., Phys.Rev. Lett. 84:2997-3000 (2000)). Indeed, evidence for better, in factnear-perfect, particle organization is obtained by in situ imaging ofthe surface after 1 μm amine-modified particles have reacted with thetemplate for 1 hour, FIG. 26.

Single particle spatial organization of particles on the micronlength-scale has been achieved by physical means, for instance usingoptical tweezers (Mio et a]., Langmuir 15:8565-8568 (1999)) or bysedimentation onto e-beam lithographically patterned polymer films (vanBlaaderen et al., Nature 385:321-323 (1997)). However, the DPN-basedmethod described here offers an advantage over previous methods becauseit provides flexibility of length scale and pattern type, as well as ameans to achieve more robust particle array structures. For instance,DPN has been used to construct chemical templates which can be utilizedto prepare square arrays of 190 nm diameter amidine-modified polystyreneparticles. Screening of the dried particle arrays using non-contact AFMor SEM imaging revealed that 300 nm template dots of MHA, spaced 570 nmapart, with a surrounding repulsive monolayer of cystamine, weresuitable for immobilizing single particles at each site in the array,FIG. 27A. However, MHA dots of diameter and spacing of 700 nm and 850 nmresulted in immobilization of multiple particles at some sites, FIG.27B.

Similar particle assembly experiments conducted at pH<5 or >9 resultedin random, non-selective particle adsorption, presumably due toprotonation of the surface acid groups or deprotonation of particleamine or amidine groups. These experiments strongly suggested that theparticle assembly process was induced by electrostatic interactionsbetween charged particles and patterned regions of the substrate.

In conclusion, it has been demonstrated that DPN can be used as a toolfor generating combinatorial chemical templates with which to positionsingle particles in two-dimensional arrays. The specific example ofcharged alkanethiols and latex particles described here will provide ageneral approach for creating two-dimensional templates for positioningsubsequent particle layers in predefined crystalline structures that maybe composed of single or multiple particle sizes and compositions. In amore general sense, the combinatorial DPN method will allow researchersto efficiently and quickly form patterned substrates with which to studyparticle-particle and particle-substrate interactions, whether theparticles are the dielectric spheres which comprise certain photonicband-gap materials, metal, semiconductor particles with potentialcatalytic or electronic properties, or even living biological cells andmacrobiomolecules.

APPENDIX

The program is written in the Microsoft Visual Basic.

This Form_DPNWrite is a core subroutine of the pattern interpreter. Theprocesses which should be done before the execution of the subroutineare:

-   -   1) Users should design patterns utilizing the user-interface        subroutine.    -   2) The patterns designed by the users should be converted into        series of dots and lines via well-known subroutines. The dots        and lines should be saved in the variables, MyDot(i) and        MyLine(i), respectively.    -   3) The diffusion constant C should be measured or retrieved from        the table for the current tip, substrate, substance and        environmental conditions, and it should be saved in the        variable, Diffusion.

The major functions of this subroutine are:

-   -   1) Calculate the holding time and speed for the basic patterns,        dots and lines, respectively.    -   2) Save the corresponding command lines in the script file.    -   3) Ask the SPM software to run the script file to perform DPN        writing. MyDot(i) is an array of DPNDot objects (class). Several        important properties of the DPNDot object are X Y, Size,        HoldTime. MyDot(i) represents a dot pattern with a radius of        MyDot(i).Size at the position of (MyDot(i)X, MyDot(i). Y).

MyLine(i) is an array of DPNLine objects (class). Several importantproperties of the DPNLine objects are X1, Y1, X2, Y2, DPNWidth, Repeat,Speed. MyLine(i) represents a line pattern connecting between (X1, Y1)and (X2, Y2) with a linewidth of DPNWidth. Repeat is an optionalparameter and its default value is 1. By specifying Repeat, users canspecify whether the line will be drawn by one or multiple sweeps of theSPM tip.

Program starts here: Public Sub Form DPNWrite( ) ‘Calculate the holdingtime for each dot and save it in MyDot(i).HoldTime.’ For i = 1 ToMyDotNum MyDot(i).HoldTime = Round(3.14159 * MyDot(i).Size *MyDot(i).Size/ Diffusion, 5) Next i ‘Calculate the speed for each lineand save it in MyLine(i).Speed.’ For i = 1 To MyLineNum MyLine(i).Speed= Round(Diffusion * MyLine(i).Repeat / MyLine(i). DPN-Width, 5) Next i‘Create the script file which will store all the command lines which canbe recognized by SPM software’ Open “c:\dpnwriting\nanoplot.scr” ForOutput As #1 ‘In the following lines, Command 1 ˜ 10 represent commandlines specific for each commercial system for the drawing system 2030,and accordingly are dependent upon, e.g, the atomic force microscopesystem utilized as the drawing system.’ ‘Add the command for the SPMsystem initialization to the script file.’ Print #1, “Command 1: Set upthe Drawing System.” Print #1, “Command 2: Separate the tip from thesubstrate.” ‘Add the commands for dot patterns to the script file.’ Fori = 1 To MyDotNum If MyDot(i).HoldTime> 0 Then Print #1, “Command 3:Move the tip to the position of the dot.” Print #1, “Command 4: Approachthe tip to make a contact with the substrate.” Print #1, “Command 5:Hold the tip for the period of MyDot(i).Hold Time.” End If Print #1,“Command 6: Separate the tip from the substrate.” Next i ‘Add thecommands for line patterns to the script file.’ For i = 1 To MyLineNumIf MyLine(i).Speed >0 Then Print #1, “Command 7: Move the tip to theinitial position, (XI, YI)” Print #1, “Command 8: Approach the tip tomake a contact with the substrate.” Print #1, “Command 9: Sweep the tipto (X2, Y2) with MyLine(:).Speed.” End If Print #1, “Command 10:Separate the tip from the substrate.” Next i Close #1 ‘Have the drawingsystem 2030 execute the commands in the script file.’ ‘The method tohave the AFM software drivers 2032 run the script file depends on thecommercial drawing system 2030 used. The following is one example whereShell Visual Basic function is utilized.’ DoDPN=Shell(“c:\spmsoftware\spmsoftware.exe-x c:\dpnwriting\- nanoplot.scr”,vbMinimizedFocus) End Sub

1-100. (canceled)
 101. A method of nanolithography comprising: providinga substrate; providing a scanning probe microscope tip; coating the tipwith a patterning compound; and using the coated tip to apply thecompound to the substrate so as to produce a desired pattern, whereinthe tip is coated with a first patterning compound and is used to applythe first patterning compound to some or all of a second patterningcompound which has already been applied to the substrate, the secondpatterning compound being capable of reacting or stably combining withthe first patterning compound.
 102. The method of claim 101 wherein thesecond patterning compound has been applied to the substrate byimmersing the substrate in a solution of the compound.
 103. A method ofnanolithography comprising: providing a substrate; providing a scanningprobe microscope tip; coating the tip with a patterning compound; andcontacting the coated tip with the substrate so that the compound isapplied to the substrate so as to produce a desired pattern, wherein thetip is coated with a first patterning compound and is used to apply thefirst patterning compound to some or all of a second patterning compoundwhich has already been applied to the substrate, the second patterningcompound being capable of reacting or stably combining with the firstpatterning compound.